rs1916636

Variant names:

• chr3-191648679-G-A
• rs1916636

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 0.378 in 151,982 control chromosomes in the GnomAD database, including 12,860 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 0.38 (12860 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 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: 0.377 AC: 57298 AN: 151864 Hom.: 12827 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.378 AC: 57391 AN: 151982 Hom.: 12860 Cov.: 32 AF XY: 0.377 AC XY: 27964 AN XY: 74268

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.333

Alfa AF: 0.274 Hom.: 10954

Bravo AF: 0.393

Asia WGS AF: 0.375 AC: 1306 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	2.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1916636; hg19: chr3-191366468;