16-79913741-C-T

Variant names:

• chr16-79913741-C-T
• rs7189172

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 0.496 in 151,634 control chromosomes in the GnomAD database, including 22,924 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 0.50 (22924 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.495 AC: 75010 AN: 151518 Hom.: 22845 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.496 AC: 75153 AN: 151634 Hom.: 22924 Cov.: 31 AF XY: 0.499 AC XY: 36931 AN XY: 74050

African (AFR) AF: 0.863 AC: 35696 AN: 41354

American (AMR) AF: 0.465 AC: 7107 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3462

East Asian (EAS) AF: 0.515 AC: 2622 AN: 5090

South Asian (SAS) AF: 0.414 AC: 1990 AN: 4808

European-Finnish (FIN) AF: 0.406 AC: 4233 AN: 10426

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21163 AN: 67912

Other (OTH) AF: 0.467 AC: 986 AN: 2110

Alfa AF: 0.392 Hom.: 5316

Bravo AF: 0.515

Asia WGS AF: 0.525 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.74
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7189172; hg19: chr16-79947638;