chr17-73837862-A-C

Variant names:

• chr17-73837862-A-C
• rs1585804

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 0.405 in 152,104 control chromosomes in the GnomAD database, including 14,429 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 0.40 (14429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.643 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: 0.405 AC: 61494 AN: 151986 Hom.: 14405 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.405 AC: 61565 AN: 152104 Hom.: 14429 Cov.: 32 AF XY: 0.400 AC XY: 29760 AN XY: 74382

African (AFR) AF: 0.650 AC: 26939 AN: 41456

American (AMR) AF: 0.330 AC: 5048 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2126 AN: 5176

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4820

European-Finnish (FIN) AF: 0.244 AC: 2585 AN: 10588

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20389 AN: 67990

Other (OTH) AF: 0.386 AC: 817 AN: 2116

Alfa AF: 0.336 Hom.: 21038

Bravo AF: 0.421

Asia WGS AF: 0.426 AC: 1484 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	1.2
DANN	Benign	0.32
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1585804; hg19: chr17-71834001;