chr17-43759814-G-C

Variant names:

• chr17-43759814-G-C
• rs851056

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 0.641 in 151,134 control chromosomes in the GnomAD database, including 31,261 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 0.64 (31261 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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: 0.640 AC: 96709 AN: 151014 Hom.: 31215 Cov.: 27

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.641 AC: 96809 AN: 151134 Hom.: 31261 Cov.: 27 AF XY: 0.644 AC XY: 47532 AN XY: 73798

African (AFR) AF: 0.673 AC: 27657 AN: 41106

American (AMR) AF: 0.572 AC: 8671 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2151 AN: 3460

East Asian (EAS) AF: 0.388 AC: 1970 AN: 5080

South Asian (SAS) AF: 0.661 AC: 3149 AN: 4766

European-Finnish (FIN) AF: 0.749 AC: 7817 AN: 10436

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43427 AN: 67828

Other (OTH) AF: 0.606 AC: 1272 AN: 2098

Alfa AF: 0.645 Hom.: 3734

Bravo AF: 0.623

Asia WGS AF: 0.528 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs851056; hg19: chr17-41837182;