rs13273442

Positions:

• chr8-42688874-A-G
• chr8-42688874-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 0.665 in 152,042 control chromosomes in the GnomAD database, including 35,789 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 0.66 (35789 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100998 AN: 151922 Hom.: 35773 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.665 AC: 101046 AN: 152042 Hom.: 35789 Cov.: 31 AF XY: 0.668 AC XY: 49662 AN XY: 74308

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.689

Alfa AF: 0.763 Hom.: 88661

Bravo AF: 0.650

Asia WGS AF: 0.713 AC: 2478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13273442; hg19: chr8-42544017;