rs2783130

Variant names:

• chr13-79596025-A-G
• rs2783130

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.380

Alfa AF: 0.404 Hom.: 3209

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

Splicing

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

Publications

LitVar

Other links and lift over

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