rs2073831

Variant names:

• chr13-76924565-C-T
• rs2073831

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 0.383 in 152,018 control chromosomes in the GnomAD database, including 13,290 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 0.38 (13290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 8 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 = 0.501 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: 0.384 AC: 58271 AN: 151900 Hom.: 13288 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.383 AC: 58282 AN: 152018 Hom.: 13290 Cov.: 32 AF XY: 0.384 AC XY: 28504 AN XY: 74292

African (AFR) AF: 0.133 AC: 5538 AN: 41526

American (AMR) AF: 0.405 AC: 6189 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1879 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1961 AN: 5162

South Asian (SAS) AF: 0.370 AC: 1785 AN: 4826

European-Finnish (FIN) AF: 0.464 AC: 4890 AN: 10538

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34338 AN: 67912

Other (OTH) AF: 0.423 AC: 894 AN: 2112

Alfa AF: 0.475 Hom.: 21190

Bravo AF: 0.373

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.75
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs2073831; hg19: chr13-77498699;