rs277522

chr16-77536452-A-Cchr16-77536452-A-Gchr16-77536452-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.893

Alfa AF: 0.920 Hom.: 77739

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs277522; hg19: chr16-77570349;