rs17077331

chr13-65782209-C-T

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 0.093 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.0548

Gnomad4 ASJ AF: 0.0871

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0463

Gnomad4 NFE AF: 0.0467

Gnomad4 OTH AF: 0.0808

Alfa AF: 0.0584 Hom.: 455

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

Splicing

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

Publications

LitVar

Other links and lift over

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