rs17077331

Variant names:

• chr13-65782209-C-T
• rs17077331

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 0.093 in 152,152 control chromosomes in the GnomAD database, including 1,021 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 0.093 (1021 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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: 0.0929 AC: 14125 AN: 152034 Hom.: 1020 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0930 AC: 14149 AN: 152152 Hom.: 1021 Cov.: 33 AF XY: 0.0914 AC XY: 6800 AN XY: 74394

African (AFR) AF: 0.201 AC: 8340 AN: 41522

American (AMR) AF: 0.0548 AC: 838 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0871 AC: 302 AN: 3466

East Asian (EAS) AF: 0.108 AC: 560 AN: 5182

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4820

European-Finnish (FIN) AF: 0.0463 AC: 491 AN: 10596

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0467 AC: 3177 AN: 67960

Other (OTH) AF: 0.0808 AC: 171 AN: 2116

Alfa AF: 0.0656 Hom.: 1368

Bravo AF: 0.100

Asia WGS AF: 0.0660 AC: 229 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.37
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs17077331; hg19: chr13-66356341; COSMIC: COSV69359555;