14-105478792-G-A

Variant names:

• chr14-105478792-G-A
• rs782271622
• NM_001312.4:c.258G>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001312.4(CRIP2):​c.258G>A​(p.Gln86Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000156 in 1,282,216 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: CRIP2 NM_001312.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 0 publications found

Genes affected

CRIP2 (HGNC:2361): (cysteine rich protein 2) This gene encodes a putative transcription factor with two LIM zinc-binding domains. The encoded protein may participate in the differentiation of smooth muscle tissue. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.011).
• BP7: Synonymous conserved (PhyloP=-3.12 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001312.4. 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
	CRIP2	NM_001312.4	MANE Select	c.258G>A	p.Gln86Gln	synonymous	Exon 4 of 8	NP_001303.1	P52943-1
	CRIP2	NM_001270837.2		c.480G>A	p.Gln160Gln	synonymous	Exon 4 of 8	NP_001257766.1	P52943-2
	CRIP2	NM_001270841.2		c.44-333G>A		intron	N/A	NP_001257770.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRIP2	ENST00000329146.9	TSL:1 MANE Select	c.258G>A	p.Gln86Gln	synonymous	Exon 4 of 8	ENSP00000328521.5	P52943-1
	CRIP2	ENST00000548309.1	TSL:1	n.1053G>A		non_coding_transcript_exon	Exon 4 of 8
	CRIP2	ENST00000483017.7	TSL:2	c.480G>A	p.Gln160Gln	synonymous	Exon 4 of 8	ENSP00000426119.2	P52943-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000156 AC: 2 AN: 1282216 Hom.: 0 Cov.: 37 AF XY: 0.00000160 AC XY: 1 AN XY: 623770

African (AFR) AF: 0.00 AC: 0 AN: 26614

American (AMR) AF: 0.00 AC: 0 AN: 19216

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18704

East Asian (EAS) AF: 0.00 AC: 0 AN: 33502

South Asian (SAS) AF: 0.00 AC: 0 AN: 62710

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31136

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3590

European-Non Finnish (NFE) AF: 0.00000193 AC: 2 AN: 1033606

Other (OTH) AF: 0.00 AC: 0 AN: 53138

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.97
PhyloP100		-3.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs782271622; hg19: chr14-105945129;