13-71318440-T-C

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 0.829 in 152,162 control chromosomes in the GnomAD database, including 52,438 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 (52438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.829 AC: 126085 AN: 152042 Hom.: 52410 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.829 AC: 126165 AN: 152162 Hom.: 52438 Cov.: 32 AF XY: 0.833 AC XY: 61964 AN XY: 74386

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.819

Alfa AF: 0.840 Hom.: 107632

Bravo AF: 0.818

Asia WGS AF: 0.848 AC: 2948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.7
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1005066; hg19: chr13-71892572;