17-43729963-T-C

Variant names:

• chr17-43729963-T-C
• rs1513670

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.603

Alfa AF: 0.630 Hom.: 68357

Bravo AF: 0.612

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1513670; hg19: chr17-41807331;