rs17295389

Variant names:

• chr13-81741664-G-A
• rs17295389

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 0.0795 in 152,150 control chromosomes in the GnomAD database, including 618 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 0.079 (618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 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: 0.0795 AC: 12090 AN: 152032 Hom.: 617 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0795 AC: 12094 AN: 152150 Hom.: 618 Cov.: 32 AF XY: 0.0782 AC XY: 5811 AN XY: 74356

African (AFR) AF: 0.0361 AC: 1500 AN: 41522

American (AMR) AF: 0.0709 AC: 1084 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.0675 AC: 325 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1152 AN: 10572

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7685 AN: 67990

Other (OTH) AF: 0.0777 AC: 164 AN: 2112

Alfa AF: 0.0857 Hom.: 128

Bravo AF: 0.0752

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.9
DANN	Benign	0.92
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs17295389; hg19: chr13-82315799;