rs17074898

Variant names:

• chr13-30711395-G-A
• rs17074898

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 0.0534 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0500

Gnomad4 AMR AF: 0.0870

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.0968

Gnomad4 FIN AF: 0.0719

Gnomad4 NFE AF: 0.0449

Gnomad4 OTH AF: 0.0508

Alfa AF: 0.0527 Hom.: 118

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17074898; hg19: chr13-31285532;