rs2291134

Variant names:

• chr8-144400142-C-A
• rs2291134
• NM_013291.3:c.937+24G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-144400142-C-A
• chr8-144400142-C-G
• chr8-144400142-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_013291.3(CPSF1):​c.937+24G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000079 (0 hom., cov: 26)
  • Exomes 𝑓: 0.000012 (2 hom.)
  • Failed GnomAD Quality Control
• Consequence: CPSF1 NM_013291.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 3 publications found

Genes affected

CPSF1 (HGNC:2324): (cleavage and polyadenylation specific factor 1) Cleavage and polyadenylation specificity factor (CPSF) is a multisubunit complex that plays a central role in 3-prime processing of pre-mRNAs. CPSF recognizes the AAUAAA signal in the pre-mRNA and interacts with other proteins to facilitate both RNA cleavage and poly(A) synthesis. CPSF1 is the largest subunit of the CPSF complex (Murthy and Manley, 1995 [PubMed 7590244]).[supplied by OMIM, Mar 2008]

MIR1234 (HGNC:33926): (microRNA 1234) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR6849 (HGNC:49991): (microRNA 6849) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.18).
• BS2: High AC in GnomAdExome4 at 14 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013291.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPSF1	NM_013291.3	MANE Select	c.937+24G>T		intron	N/A	NP_037423.2	Q10570
	MIR1234	NR_031600.2		n.24G>T		non_coding_transcript_exon	Exon 1 of 1
	MIR6849	NR_106908.1		n.*135G>T		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPSF1	ENST00000616140.2	TSL:1 MANE Select	c.937+24G>T		intron	N/A	ENSP00000484669.1	Q10570
	CPSF1	ENST00000620219.4	TSL:1	c.937+24G>T		intron	N/A	ENSP00000478145.1	Q10570
	CPSF1	ENST00000886816.1		c.937+24G>T		intron	N/A	ENSP00000556875.1

Frequencies

GnomAD3 genomes AF: 0.00000786 AC: 1 AN: 127252 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000186

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000125 AC: 14 AN: 1120950 Hom.: 2 Cov.: 19 AF XY: 0.00000897 AC XY: 5 AN XY: 557452

African (AFR) AF: 0.00 AC: 0 AN: 27280

American (AMR) AF: 0.00 AC: 0 AN: 32564

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20452

East Asian (EAS) AF: 0.00 AC: 0 AN: 34896

South Asian (SAS) AF: 0.00 AC: 0 AN: 69208

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39310

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3362

European-Non Finnish (NFE) AF: 0.0000166 AC: 14 AN: 845332

Other (OTH) AF: 0.00 AC: 0 AN: 48546

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000786 AC: 1 AN: 127252 Hom.: 0 Cov.: 26 AF XY: 0.0000161 AC XY: 1 AN XY: 62140

African (AFR) AF: 0.00 AC: 0 AN: 36180

American (AMR) AF: 0.00 AC: 0 AN: 13672

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2854

East Asian (EAS) AF: 0.00 AC: 0 AN: 4482

South Asian (SAS) AF: 0.00 AC: 0 AN: 3756

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9892

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 282

European-Non Finnish (NFE) AF: 0.0000186 AC: 1 AN: 53758

Other (OTH) AF: 0.00 AC: 0 AN: 1688

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.18
PhyloP100		-2.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2291134;