rs17078046

Variant names:

• chr13-23012112-G-A
• rs17078046

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 0.132 in 151,904 control chromosomes in the GnomAD database, including 1,658 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 0.13 (1658 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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: 0.132 AC: 20071 AN: 151792 Hom.: 1648 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00776

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0811

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.132 AC: 20111 AN: 151904 Hom.: 1658 Cov.: 31 AF XY: 0.132 AC XY: 9813 AN XY: 74252

African (AFR) AF: 0.219 AC: 9074 AN: 41384

American (AMR) AF: 0.152 AC: 2320 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3468

East Asian (EAS) AF: 0.00778 AC: 40 AN: 5140

South Asian (SAS) AF: 0.0857 AC: 412 AN: 4806

European-Finnish (FIN) AF: 0.0811 AC: 854 AN: 10532

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6625 AN: 68002

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.135 Hom.: 226

Bravo AF: 0.138

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.38
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs17078046; hg19: chr13-23586251;