rs4902642

Variant names:

• chr14-68743482-G-A
• rs4902642

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.371 in 151,950 control chromosomes in the GnomAD database, including 10,933 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 0.37 (10933 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56286 AN: 151832 Hom.: 10924 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.371 AC: 56318 AN: 151950 Hom.: 10933 Cov.: 31 AF XY: 0.374 AC XY: 27758 AN XY: 74272

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.369

Alfa AF: 0.405 Hom.: 29067

Bravo AF: 0.348

Asia WGS AF: 0.388 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	9.3
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902642; hg19: chr14-69210199;