rs1999494

Variant names:

• chr13-80426370-G-A
• rs1999494

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 0.364 in 151,950 control chromosomes in the GnomAD database, including 10,142 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 (10142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55331 AN: 151832 Hom.: 10135 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.364 AC: 55364 AN: 151950 Hom.: 10142 Cov.: 32 AF XY: 0.366 AC XY: 27152 AN XY: 74256

African (AFR) AF: 0.391 AC: 16217 AN: 41440

American (AMR) AF: 0.322 AC: 4918 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2202 AN: 5158

South Asian (SAS) AF: 0.469 AC: 2259 AN: 4820

European-Finnish (FIN) AF: 0.351 AC: 3706 AN: 10552

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.347 AC: 23593 AN: 67930

Other (OTH) AF: 0.364 AC: 766 AN: 2106

Alfa AF: 0.348 Hom.: 34351

Bravo AF: 0.358

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.75
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs1999494; hg19: chr13-81000505;