chr17-70189445-G-A

Variant names:

• chr17-70189445-G-A
• rs8080944

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 0.554 in 151,768 control chromosomes in the GnomAD database, including 23,535 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 0.55 (23535 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 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: 0.554 AC: 84004 AN: 151650 Hom.: 23504 Cov.: 31

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.554 AC: 84084 AN: 151768 Hom.: 23535 Cov.: 31 AF XY: 0.551 AC XY: 40873 AN XY: 74162

African (AFR) AF: 0.480 AC: 19842 AN: 41344

American (AMR) AF: 0.512 AC: 7808 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1969 AN: 3466

East Asian (EAS) AF: 0.611 AC: 3139 AN: 5140

South Asian (SAS) AF: 0.578 AC: 2782 AN: 4812

European-Finnish (FIN) AF: 0.602 AC: 6343 AN: 10530

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40296 AN: 67918

Other (OTH) AF: 0.545 AC: 1150 AN: 2112

Alfa AF: 0.574 Hom.: 36279

Bravo AF: 0.541

Asia WGS AF: 0.594 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8080944; hg19: chr17-68185586; COSMIC: COSV107162152;