rs1841359

Variant names:

• chr13-72015935-G-A
• rs1841359

Your query was ambiguous. Multiple possible variants found:

• chr13-72015935-G-A
• chr13-72015935-G-C

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 0.339 in 152,010 control chromosomes in the GnomAD database, including 9,812 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 0.34 (9812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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: 0.339 AC: 51517 AN: 151892 Hom.: 9794 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.339 AC: 51579 AN: 152010 Hom.: 9812 Cov.: 32 AF XY: 0.337 AC XY: 25027 AN XY: 74288

African (AFR) AF: 0.527 AC: 21843 AN: 41442

American (AMR) AF: 0.291 AC: 4451 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3466

East Asian (EAS) AF: 0.327 AC: 1688 AN: 5162

South Asian (SAS) AF: 0.312 AC: 1506 AN: 4822

European-Finnish (FIN) AF: 0.247 AC: 2605 AN: 10552

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17906 AN: 67982

Other (OTH) AF: 0.342 AC: 721 AN: 2110

Alfa AF: 0.312 Hom.: 2376

Bravo AF: 0.350

Asia WGS AF: 0.371 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.30
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1841359; hg19: chr13-72590073;