rs6497436

Variant names:

• chr16-20112193-T-C
• rs6497436

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.789 in 152,196 control chromosomes in the GnomAD database, including 47,622 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 0.79 (47622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.87
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 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: 0.789 AC: 119929 AN: 152078 Hom.: 47570 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.789 AC: 120040 AN: 152196 Hom.: 47622 Cov.: 32 AF XY: 0.787 AC XY: 58564 AN XY: 74408

African (AFR) AF: 0.882 AC: 36616 AN: 41536

American (AMR) AF: 0.765 AC: 11690 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2936 AN: 3472

East Asian (EAS) AF: 0.733 AC: 3788 AN: 5166

South Asian (SAS) AF: 0.790 AC: 3814 AN: 4826

European-Finnish (FIN) AF: 0.735 AC: 7789 AN: 10594

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50920 AN: 67996

Other (OTH) AF: 0.797 AC: 1687 AN: 2116

Alfa AF: 0.799 Hom.: 26975

Bravo AF: 0.794

Asia WGS AF: 0.769 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.43
PhyloP100		-4.9

Splicing

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

Other links and lift over

dbSNP: rs6497436; hg19: chr16-20123515;