rs1935099

Variant names:

• chr13-36396790-G-A
• rs1935099

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 0.439 in 151,910 control chromosomes in the GnomAD database, including 14,875 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 0.44 (14875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 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: 0.440 AC: 66716 AN: 151792 Hom.: 14871 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.439 AC: 66752 AN: 151910 Hom.: 14875 Cov.: 32 AF XY: 0.437 AC XY: 32485 AN XY: 74262

African (AFR) AF: 0.353 AC: 14625 AN: 41412

American (AMR) AF: 0.491 AC: 7488 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3466

East Asian (EAS) AF: 0.407 AC: 2107 AN: 5174

South Asian (SAS) AF: 0.445 AC: 2147 AN: 4824

European-Finnish (FIN) AF: 0.445 AC: 4684 AN: 10530

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32726 AN: 67940

Other (OTH) AF: 0.436 AC: 919 AN: 2108

Alfa AF: 0.468 Hom.: 66321

Bravo AF: 0.442

Asia WGS AF: 0.425 AC: 1479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs1935099; hg19: chr13-36970927;