rs277522

Variant names:

• chr16-77536452-A-C
• rs277522

Your query was ambiguous. Multiple possible variants found:

• chr16-77536452-A-C
• chr16-77536452-A-G
• chr16-77536452-A-T

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 0.921 in 151,906 control chromosomes in the GnomAD database, including 64,465 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 0.92 (64465 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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: 0.921 AC: 139752 AN: 151788 Hom.: 64414 Cov.: 28

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.921 AC: 139858 AN: 151906 Hom.: 64465 Cov.: 28 AF XY: 0.920 AC XY: 68254 AN XY: 74220

African (AFR) AF: 0.925 AC: 38283 AN: 41390

American (AMR) AF: 0.885 AC: 13513 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2910 AN: 3470

East Asian (EAS) AF: 0.968 AC: 4966 AN: 5128

South Asian (SAS) AF: 0.881 AC: 4179 AN: 4744

European-Finnish (FIN) AF: 0.942 AC: 9970 AN: 10582

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 63007 AN: 68012

Other (OTH) AF: 0.893 AC: 1883 AN: 2108

Alfa AF: 0.920 Hom.: 100577

Bravo AF: 0.918

Asia WGS AF: 0.939 AC: 3265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.73
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs277522; hg19: chr16-77570349;