chr13-70353943-G-T

Variant names:

• chr13-70353943-G-T
• rs9599646

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 0.397 in 151,864 control chromosomes in the GnomAD database, including 12,110 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 0.40 (12110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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: 0.397 AC: 60249 AN: 151744 Hom.: 12112 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.397 AC: 60269 AN: 151864 Hom.: 12110 Cov.: 32 AF XY: 0.390 AC XY: 28907 AN XY: 74206

African (AFR) AF: 0.405 AC: 16769 AN: 41448

American (AMR) AF: 0.384 AC: 5848 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1365 AN: 3462

East Asian (EAS) AF: 0.443 AC: 2270 AN: 5124

South Asian (SAS) AF: 0.363 AC: 1749 AN: 4822

European-Finnish (FIN) AF: 0.292 AC: 3083 AN: 10550

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27947 AN: 67920

Other (OTH) AF: 0.387 AC: 815 AN: 2106

Alfa AF: 0.396 Hom.: 1680

Bravo AF: 0.402

Asia WGS AF: 0.390 AC: 1354 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9599646; hg19: chr13-70928075;