chr16-77524780-A-G

Variant names:

• chr16-77524780-A-G
• rs8057501

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 0.375 in 151,986 control chromosomes in the GnomAD database, including 10,969 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 0.38 (10969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56985 AN: 151868 Hom.: 10962 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.375 AC: 57019 AN: 151986 Hom.: 10969 Cov.: 32 AF XY: 0.374 AC XY: 27759 AN XY: 74278

African (AFR) AF: 0.388 AC: 16077 AN: 41426

American (AMR) AF: 0.314 AC: 4800 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3468

East Asian (EAS) AF: 0.132 AC: 682 AN: 5174

South Asian (SAS) AF: 0.419 AC: 2017 AN: 4816

European-Finnish (FIN) AF: 0.395 AC: 4171 AN: 10570

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26626 AN: 67940

Other (OTH) AF: 0.351 AC: 740 AN: 2106

Alfa AF: 0.382 Hom.: 38367

Bravo AF: 0.365

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8057501; hg19: chr16-77558677;