rs7201962

Variant names:

• chr16-24585849-A-G
• rs7201962

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 0.337 in 151,960 control chromosomes in the GnomAD database, including 10,482 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 0.34 (10482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.337 AC: 51102 AN: 151842 Hom.: 10462 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.337 AC: 51172 AN: 151960 Hom.: 10482 Cov.: 32 AF XY: 0.335 AC XY: 24853 AN XY: 74276

African (AFR) AF: 0.582 AC: 24093 AN: 41384

American (AMR) AF: 0.247 AC: 3773 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3466

East Asian (EAS) AF: 0.199 AC: 1023 AN: 5146

South Asian (SAS) AF: 0.346 AC: 1663 AN: 4808

European-Finnish (FIN) AF: 0.246 AC: 2596 AN: 10572

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16346 AN: 67986

Other (OTH) AF: 0.297 AC: 627 AN: 2110

Alfa AF: 0.270 Hom.: 19963

Bravo AF: 0.344

Asia WGS AF: 0.320 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs7201962; hg19: chr16-24597170;