chr17-43729963-T-C

Variant names:

• chr17-43729963-T-C
• rs1513670

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 0.63 in 151,928 control chromosomes in the GnomAD database, including 30,433 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 0.63 (30433 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 44 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 (SAS) allele frequency at 95% confidence interval = 0.67 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: 0.630 AC: 95572 AN: 151810 Hom.: 30380 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.630 AC: 95674 AN: 151928 Hom.: 30433 Cov.: 31 AF XY: 0.634 AC XY: 47066 AN XY: 74234

African (AFR) AF: 0.609 AC: 25217 AN: 41414

American (AMR) AF: 0.593 AC: 9053 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2179 AN: 5170

South Asian (SAS) AF: 0.690 AC: 3324 AN: 4820

European-Finnish (FIN) AF: 0.764 AC: 8057 AN: 10540

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43625 AN: 67940

Other (OTH) AF: 0.603 AC: 1274 AN: 2112

Alfa AF: 0.632 Hom.: 143081

Bravo AF: 0.612

Asia WGS AF: 0.561 AC: 1950 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	0.71
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1513670; hg19: chr17-41807331;