rs1999494

Variant names:

• chr13-80426370-G-A
• rs1999494

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.364 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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.364

Alfa AF: 0.346 Hom.: 13726

Bravo AF: 0.358

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1999494; hg19: chr13-81000505;