13-71336784-C-G

Variant names:

• chr13-71336784-C-G
• rs1931443

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 0.232 in 151,686 control chromosomes in the GnomAD database, including 5,081 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 0.23 (5081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 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: 0.232 AC: 35136 AN: 151568 Hom.: 5083 Cov.: 32

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.232 AC: 35134 AN: 151686 Hom.: 5081 Cov.: 32 AF XY: 0.238 AC XY: 17611 AN XY: 74128

African (AFR) AF: 0.0572 AC: 2369 AN: 41436

American (AMR) AF: 0.323 AC: 4906 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3466

East Asian (EAS) AF: 0.165 AC: 854 AN: 5162

South Asian (SAS) AF: 0.385 AC: 1852 AN: 4816

European-Finnish (FIN) AF: 0.349 AC: 3677 AN: 10528

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19948 AN: 67798

Other (OTH) AF: 0.222 AC: 467 AN: 2106

Alfa AF: 0.152 Hom.: 318

Bravo AF: 0.220

Asia WGS AF: 0.296 AC: 1026 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.39
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1931443; hg19: chr13-71910916;