rs2783130

Variant names:

• chr13-79596025-A-G
• rs2783130

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.36 in 151,894 control chromosomes in the GnomAD database, including 11,831 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 0.36 (11831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 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: 0.361 AC: 54734 AN: 151776 Hom.: 11839 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.360 AC: 54714 AN: 151894 Hom.: 11831 Cov.: 32 AF XY: 0.361 AC XY: 26809 AN XY: 74196

African (AFR) AF: 0.121 AC: 5014 AN: 41458

American (AMR) AF: 0.331 AC: 5052 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1678 AN: 3466

East Asian (EAS) AF: 0.306 AC: 1579 AN: 5162

South Asian (SAS) AF: 0.526 AC: 2529 AN: 4810

European-Finnish (FIN) AF: 0.472 AC: 4974 AN: 10532

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.480 AC: 32609 AN: 67902

Other (OTH) AF: 0.380 AC: 800 AN: 2108

Alfa AF: 0.406 Hom.: 5511

Bravo AF: 0.338

Asia WGS AF: 0.385 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	18
DANN	Benign	0.79
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs2783130; hg19: chr13-80170160; COSMIC: COSV69618357;