17-81485136-G-T

Variant names:

• chr17-81485136-G-T
• rs9907460

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 0.615 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.565 AC: 23445 AN: 41486

American (AMR) AF: 0.675 AC: 10306 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2330 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3623 AN: 5182

South Asian (SAS) AF: 0.719 AC: 3467 AN: 4824

European-Finnish (FIN) AF: 0.610 AC: 6440 AN: 10566

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42026 AN: 67996

Other (OTH) AF: 0.630 AC: 1329 AN: 2110

Alfa AF: 0.602 Hom.: 8179

Bravo AF: 0.614

Asia WGS AF: 0.704 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.58
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9907460; hg19: chr17-79452162;