chr17-47754581-C-T

Variant names:

• chr17-47754581-C-T
• rs41515744

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 0.102 in 152,180 control chromosomes in the GnomAD database, including 855 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 0.10 (855 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 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: 0.102 AC: 15549 AN: 152062 Hom.: 852 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.0606

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0740

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0890

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.102 AC: 15564 AN: 152180 Hom.: 855 Cov.: 31 AF XY: 0.104 AC XY: 7752 AN XY: 74398

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0953

Gnomad4 EAS AF: 0.0604

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0740

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.0936

Alfa AF: 0.0939 Hom.: 151

Bravo AF: 0.103

Asia WGS AF: 0.146 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41515744; hg19: chr17-45831947;