13-90242741-A-T

Variant names:

• chr13-90242741-A-T
• rs9670398

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 0.718 in 151,956 control chromosomes in the GnomAD database, including 39,445 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 0.72 (39445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 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: 0.718 AC: 109086 AN: 151840 Hom.: 39418 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.718 AC: 109173 AN: 151956 Hom.: 39445 Cov.: 32 AF XY: 0.712 AC XY: 52917 AN XY: 74300

African (AFR) AF: 0.706 AC: 29292 AN: 41476

American (AMR) AF: 0.705 AC: 10745 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2418 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2442 AN: 5164

South Asian (SAS) AF: 0.648 AC: 3126 AN: 4822

European-Finnish (FIN) AF: 0.699 AC: 7368 AN: 10548

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51349 AN: 67922

Other (OTH) AF: 0.713 AC: 1505 AN: 2110

Alfa AF: 0.734 Hom.: 5112

Bravo AF: 0.717

Asia WGS AF: 0.582 AC: 2019 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.83
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9670398; hg19: chr13-90894995;