17-43729963-T-C

Position:

• chr17-43729963-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;