17-77012989-G-A

Variant names:

• chr17-77012989-G-A
• rs6501930

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 0.817 in 152,230 control chromosomes in the GnomAD database, including 51,249 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 0.82 (51249 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124318 AN: 152112 Hom.: 51203 Cov.: 34

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.817 AC: 124417 AN: 152230 Hom.: 51249 Cov.: 34 AF XY: 0.814 AC XY: 60540 AN XY: 74404

African (AFR) AF: 0.914 AC: 38002 AN: 41562

American (AMR) AF: 0.777 AC: 11883 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2831 AN: 3466

East Asian (EAS) AF: 0.765 AC: 3969 AN: 5186

South Asian (SAS) AF: 0.698 AC: 3365 AN: 4824

European-Finnish (FIN) AF: 0.783 AC: 8278 AN: 10572

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53480 AN: 68004

Other (OTH) AF: 0.807 AC: 1707 AN: 2116

Alfa AF: 0.794 Hom.: 29231

Bravo AF: 0.824

Asia WGS AF: 0.699 AC: 2434 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	1.1
DANN	Benign	0.092
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6501930; hg19: chr17-75009071;