rs4903696

Variant names:

• chr14-78050017-C-A
• rs4903696

Your query was ambiguous. Multiple possible variants found:

• chr14-78050017-C-A
• chr14-78050017-C-G
• chr14-78050017-C-T

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 0.512 in 152,072 control chromosomes in the GnomAD database, including 20,565 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 0.51 (20565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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: 0.512 AC: 77756 AN: 151954 Hom.: 20530 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.512 AC: 77849 AN: 152072 Hom.: 20565 Cov.: 32 AF XY: 0.513 AC XY: 38104 AN XY: 74346

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.521

Alfa AF: 0.466 Hom.: 8025

Bravo AF: 0.514

Asia WGS AF: 0.602 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4903696; hg19: chr14-78516360; COSMIC: COSV59174355;