17-81485136-G-T

Variant names:

• chr17-81485136-G-T
• rs9907460

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 0.615 in 152,118 control chromosomes in the GnomAD database, including 28,966 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 0.62 (28966 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 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: 0.615 AC: 93492 AN: 152000 Hom.: 28934 Cov.: 34

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.615 AC: 93568 AN: 152118 Hom.: 28966 Cov.: 34 AF XY: 0.618 AC XY: 45954 AN XY: 74370

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.630

Alfa AF: 0.571 Hom.: 3285

Bravo AF: 0.614

Asia WGS AF: 0.704 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9907460; hg19: chr17-79452162;