rs117432838

Variant names:

• chr10-10796888-A-T
• rs117432838
• NM_001326324.2:c.-71A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-10796888-A-T
• chr10-10796888-A-C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001326324.2(CELF2):​c.-71A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0496 in 984,392 control chromosomes in the GnomAD database, including 1,364 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.035 (149 hom., cov: 32)
  • Exomes 𝑓: 0.052 (1215 hom.)
• Consequence: CELF2 NM_001326324.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.335
• Publications: 1 publications found

Genes affected

CELF2 (HGNC:2550): (CUGBP Elav-like family member 2) Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

SFTA1P (HGNC:18383): (surfactant associated 1, lncRNA)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 10-10796888-A-T is Benign according to our data. Variant chr10-10796888-A-T is described in ClinVar as Benign. ClinVar VariationId is 770961.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001326324.2. 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
	CELF2	NM_001326324.2		c.-71A>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 15	NP_001313253.1	O95319-2
	CELF2	NM_001326325.2		c.1A>T	p.Met1?	initiator_codon	Exon 1 of 16	NP_001313254.1
	CELF2	NM_001326324.2		c.-71A>T		5_prime_UTR	Exon 1 of 15	NP_001313253.1	O95319-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTA1P	ENST00000739709.1		n.102+1650T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0349 AC: 5313 AN: 152210 Hom.: 149 Cov.: 32

Gnomad AFR AF: 0.00842

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0206

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0189

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.0523 AC: 43558 AN: 832064 Hom.: 1215 Cov.: 26 AF XY: 0.0524 AC XY: 20152 AN XY: 384270

African (AFR) AF: 0.00608 AC: 96 AN: 15782

American (AMR) AF: 0.0153 AC: 15 AN: 982

Ashkenazi Jewish (ASJ) AF: 0.00563 AC: 29 AN: 5152

East Asian (EAS) AF: 0.000275 AC: 1 AN: 3630

South Asian (SAS) AF: 0.0200 AC: 329 AN: 16450

European-Finnish (FIN) AF: 0.0870 AC: 24 AN: 276

Middle Eastern (MID) AF: 0.00988 AC: 16 AN: 1620

European-Non Finnish (NFE) AF: 0.0551 AC: 41941 AN: 760896

Other (OTH) AF: 0.0406 AC: 1107 AN: 27276

GnomAD4 genome AF: 0.0349 AC: 5314 AN: 152328 Hom.: 149 Cov.: 32 AF XY: 0.0349 AC XY: 2596 AN XY: 74484

African (AFR) AF: 0.00839 AC: 349 AN: 41590

American (AMR) AF: 0.0207 AC: 316 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00403 AC: 14 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0187 AC: 90 AN: 4822

European-Finnish (FIN) AF: 0.0723 AC: 767 AN: 10612

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0537 AC: 3653 AN: 68026

Other (OTH) AF: 0.0198 AC: 42 AN: 2116

Alfa AF: 0.0400 Hom.: 15

Bravo AF: 0.0306

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.0
DANN	Benign	0.75
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs117432838; hg19: chr10-10838851; COSMIC: COSV70289346;