rs16959642

Variant names:

• chr16-58022977-T-C
• rs16959642

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 0.124 in 152,182 control chromosomes in the GnomAD database, including 1,343 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 0.12 (1343 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 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: 0.124 AC: 18833 AN: 152064 Hom.: 1341 Cov.: 33

Gnomad AFR AF: 0.0730

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.124 AC: 18833 AN: 152182 Hom.: 1343 Cov.: 33 AF XY: 0.123 AC XY: 9176 AN XY: 74404

African (AFR) AF: 0.0730 AC: 3031 AN: 41534

American (AMR) AF: 0.116 AC: 1776 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3472

East Asian (EAS) AF: 0.123 AC: 638 AN: 5168

South Asian (SAS) AF: 0.131 AC: 631 AN: 4828

European-Finnish (FIN) AF: 0.136 AC: 1443 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10344 AN: 67976

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.138 Hom.: 2422

Bravo AF: 0.118

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs16959642; hg19: chr16-58056881;