13-71872548-A-G

Variant names:

• chr13-71872548-A-G
• rs3818437

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 0.833 in 152,034 control chromosomes in the GnomAD database, including 56,347 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 0.83 (56347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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: 0.833 AC: 126576 AN: 151916 Hom.: 56342 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.833 AC: 126620 AN: 152034 Hom.: 56347 Cov.: 32 AF XY: 0.834 AC XY: 61971 AN XY: 74314

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.865

Alfa AF: 0.899 Hom.: 7016

Bravo AF: 0.809

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3818437; hg19: chr13-72446686;