16-75213347-T-G

Variant names:

• chr16-75213347-T-G
• rs7202877

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 0.128 in 152,262 control chromosomes in the GnomAD database, including 1,383 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 0.13 (1383 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507
• Publications: 182 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 (EAS) allele frequency at 95% confidence interval = 0.192 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: 0.128 AC: 19507 AN: 152144 Hom.: 1370 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.128 AC: 19538 AN: 152262 Hom.: 1383 Cov.: 33 AF XY: 0.128 AC XY: 9524 AN XY: 74464

African (AFR) AF: 0.180 AC: 7475 AN: 41530

American (AMR) AF: 0.104 AC: 1584 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0763 AC: 265 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1047 AN: 5182

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4828

European-Finnish (FIN) AF: 0.139 AC: 1478 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6919 AN: 68016

Other (OTH) AF: 0.126 AC: 267 AN: 2116

Alfa AF: 0.107 Hom.: 4486

Bravo AF: 0.129

Asia WGS AF: 0.157 AC: 547 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	1.1
DANN	Benign	0.27
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs7202877; hg19: chr16-75247245;