rs694936

Variant names:

• chr3-101868949-T-A
• rs694936

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 0.361 in 152,056 control chromosomes in the GnomAD database, including 10,561 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 0.36 (10561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 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: 0.361 AC: 54872 AN: 151938 Hom.: 10560 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.361 AC: 54884 AN: 152056 Hom.: 10561 Cov.: 32 AF XY: 0.353 AC XY: 26227 AN XY: 74322

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.370

Alfa AF: 0.381 Hom.: 1426

Bravo AF: 0.362

Asia WGS AF: 0.306 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs694936; hg19: chr3-101587793;