chr17-78926196-G-A

Variant names:

• chr17-78926196-G-A
• rs8080623

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 0.843 in 152,080 control chromosomes in the GnomAD database, including 55,420 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 0.84 (55420 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128085 AN: 151962 Hom.: 55402 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.843 AC: 128146 AN: 152080 Hom.: 55420 Cov.: 31 AF XY: 0.842 AC XY: 62591 AN XY: 74342

African (AFR) AF: 0.633 AC: 26219 AN: 41428

American (AMR) AF: 0.927 AC: 14160 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3262 AN: 3466

East Asian (EAS) AF: 0.761 AC: 3921 AN: 5150

South Asian (SAS) AF: 0.788 AC: 3802 AN: 4824

European-Finnish (FIN) AF: 0.932 AC: 9874 AN: 10598

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63942 AN: 68018

Other (OTH) AF: 0.853 AC: 1799 AN: 2110

Alfa AF: 0.851 Hom.: 7048

Bravo AF: 0.836

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.2
DANN	Benign	0.69
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs8080623; hg19: chr17-76922278;