13-71889403-G-A

Position:

• chr13-71889403-G-A

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 0.84 in 152,096 control chromosomes in the GnomAD database, including 56,942 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 0.84 (56942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

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 (NFE) allele frequency at 95% confidence interval = 0.99 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: 0.840 AC: 127638 AN: 151976 Hom.: 56935 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.840 AC: 127693 AN: 152096 Hom.: 56942 Cov.: 32 AF XY: 0.840 AC XY: 62438 AN XY: 74360

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.872

Alfa AF: 0.935 Hom.: 19361

Bravo AF: 0.817

Asia WGS AF: 0.756 AC: 2621 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1460465; hg19: chr13-72463541;