rs17078161

Variant names:

• chr13-23076159-A-G
• rs17078161

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 0.142 in 152,210 control chromosomes in the GnomAD database, including 1,789 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 0.14 (1789 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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: 0.142 AC: 21609 AN: 152092 Hom.: 1786 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.142 AC: 21647 AN: 152210 Hom.: 1789 Cov.: 32 AF XY: 0.143 AC XY: 10605 AN XY: 74414

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0462

Gnomad4 SAS AF: 0.0996

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.139

Alfa AF: 0.118 Hom.: 1909

Bravo AF: 0.145

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17078161; hg19: chr13-23650298;