13-71196509-T-C

Variant names:

• chr13-71196509-T-C
• rs768826

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.493 in 151,928 control chromosomes in the GnomAD database, including 19,946 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 0.49 (19946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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: 0.493 AC: 74834 AN: 151810 Hom.: 19915 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.493 AC: 74913 AN: 151928 Hom.: 19946 Cov.: 32 AF XY: 0.482 AC XY: 35821 AN XY: 74250

African (AFR) AF: 0.707 AC: 29324 AN: 41472

American (AMR) AF: 0.361 AC: 5500 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1461 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2234 AN: 5164

South Asian (SAS) AF: 0.263 AC: 1265 AN: 4816

European-Finnish (FIN) AF: 0.372 AC: 3929 AN: 10574

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29802 AN: 67892

Other (OTH) AF: 0.449 AC: 946 AN: 2108

Alfa AF: 0.482 Hom.: 3674

Bravo AF: 0.503

Asia WGS AF: 0.373 AC: 1293 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.55
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs768826; hg19: chr13-71770641;