rs1913208

Variant names:

• chr13-104069439-T-G
• rs1913208

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 0.53 in 151,880 control chromosomes in the GnomAD database, including 23,093 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 0.53 (23093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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: 0.530 AC: 80421 AN: 151762 Hom.: 23062 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.530 AC: 80506 AN: 151880 Hom.: 23093 Cov.: 32 AF XY: 0.519 AC XY: 38490 AN XY: 74230

African (AFR) AF: 0.753 AC: 31185 AN: 41418

American (AMR) AF: 0.452 AC: 6895 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1544 AN: 3464

East Asian (EAS) AF: 0.358 AC: 1847 AN: 5158

South Asian (SAS) AF: 0.361 AC: 1736 AN: 4808

European-Finnish (FIN) AF: 0.367 AC: 3856 AN: 10518

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31735 AN: 67946

Other (OTH) AF: 0.517 AC: 1090 AN: 2108

Alfa AF: 0.488 Hom.: 58139

Bravo AF: 0.546

Asia WGS AF: 0.394 AC: 1373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1913208; hg19: chr13-104721789;