rs17074898

Variant names:

• chr13-30711395-G-A
• rs17074898

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 0.0534 in 152,246 control chromosomes in the GnomAD database, including 249 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 0.053 (249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0895 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: 0.0533 AC: 8112 AN: 152128 Hom.: 249 Cov.: 32

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0449

Gnomad OTH AF: 0.0513

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

GnomAD4 genome AF: 0.0534 AC: 8125 AN: 152246 Hom.: 249 Cov.: 32 AF XY: 0.0566 AC XY: 4210 AN XY: 74428

African (AFR) AF: 0.0500 AC: 2080 AN: 41560

American (AMR) AF: 0.0870 AC: 1330 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.0235 AC: 122 AN: 5186

South Asian (SAS) AF: 0.0968 AC: 467 AN: 4826

European-Finnish (FIN) AF: 0.0719 AC: 761 AN: 10578

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0449 AC: 3055 AN: 68020

Other (OTH) AF: 0.0508 AC: 107 AN: 2108

Alfa AF: 0.0529 Hom.: 141

Bravo AF: 0.0518

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.65
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs17074898; hg19: chr13-31285532;