chr17-71403132-T-C

Position:

• chr17-71403132-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 0.937 in 152,238 control chromosomes in the GnomAD database, including 67,395 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 0.94 (67395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 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: 0.937 AC: 142479 AN: 152120 Hom.: 67332 Cov.: 32

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.937 AC: 142603 AN: 152238 Hom.: 67395 Cov.: 32 AF XY: 0.932 AC XY: 69351 AN XY: 74422

Gnomad4 AFR AF: 0.976

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.936

Alfa AF: 0.948 Hom.: 29803

Bravo AF: 0.935

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.071
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs917344; hg19: chr17-69399273;