rs13277524

Variant names:

• chr8-42694914-G-T
• rs13277524

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 0.639 in 152,162 control chromosomes in the GnomAD database, including 34,344 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 0.64 (34344 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 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: 0.639 AC: 97184 AN: 152042 Hom.: 34333 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.639 AC: 97221 AN: 152162 Hom.: 34344 Cov.: 33 AF XY: 0.644 AC XY: 47885 AN XY: 74382

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.673

Alfa AF: 0.695 Hom.: 4838

Bravo AF: 0.620

Asia WGS AF: 0.710 AC: 2469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13277524; hg19: chr8-42550057;