rs1916636

Positions:

• chr3-191648679-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;