rs2793701

Variant names:

• chr13-97748352-C-A
• rs2793701

Your query was ambiguous. Multiple possible variants found:

• chr13-97748352-C-A
• chr13-97748352-C-T

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 0.308 in 151,772 control chromosomes in the GnomAD database, including 7,412 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 0.31 (7412 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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: 0.308 AC: 46739 AN: 151654 Hom.: 7398 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.308 AC: 46787 AN: 151772 Hom.: 7412 Cov.: 31 AF XY: 0.305 AC XY: 22612 AN XY: 74202

African (AFR) AF: 0.339 AC: 14044 AN: 41376

American (AMR) AF: 0.272 AC: 4146 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1201 AN: 3468

East Asian (EAS) AF: 0.0792 AC: 407 AN: 5136

South Asian (SAS) AF: 0.260 AC: 1248 AN: 4804

European-Finnish (FIN) AF: 0.263 AC: 2766 AN: 10520

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.323 AC: 21936 AN: 67906

Other (OTH) AF: 0.313 AC: 661 AN: 2112

Alfa AF: 0.315 Hom.: 21792

Bravo AF: 0.310

Asia WGS AF: 0.191 AC: 668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.56
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2793701; hg19: chr13-98400606;