rs4902141

Variant names:

• chr14-62501677-T-C
• rs4902141
• ENST00000743723.1:n.587-2367T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000743723.1(ENSG00000296937):​n.587-2367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 152,346 control chromosomes in the GnomAD database, including 81 homozygotes. 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 0.024 (81 hom., cov: 33)
• Consequence: ENSG00000296937 ENST00000743723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 2 publications found

Genes affected

ENSG00000296937 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0239 (3635/152346) while in subpopulation SAS AF = 0.0412 (199/4828). AF 95% confidence interval is 0.0365. There are 81 homozygotes in GnomAd4. There are 1768 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 81 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743723.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296937	ENST00000743723.1		n.587-2367T>C		intron	N/A
	ENSG00000296937	ENST00000743724.1		n.588-2367T>C		intron	N/A
	ENSG00000296937	ENST00000743725.1		n.333-2364T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3623 AN: 152228 Hom.: 79 Cov.: 33

Gnomad AFR AF: 0.00680

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0181

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0239 AC: 3635 AN: 152346 Hom.: 81 Cov.: 33 AF XY: 0.0237 AC XY: 1768 AN XY: 74500

African (AFR) AF: 0.00678 AC: 282 AN: 41580

American (AMR) AF: 0.0180 AC: 276 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3468

East Asian (EAS) AF: 0.0200 AC: 104 AN: 5188

South Asian (SAS) AF: 0.0412 AC: 199 AN: 4828

European-Finnish (FIN) AF: 0.0241 AC: 256 AN: 10624

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0340 AC: 2314 AN: 68030

Other (OTH) AF: 0.0307 AC: 65 AN: 2114

Alfa AF: 0.0309 Hom.: 146

Bravo AF: 0.0231

Asia WGS AF: 0.0480 AC: 166 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs4902141; hg19: chr14-62968395;