17-39453870-T-C

Position:

• chr17-39453870-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 0.162 in 152,090 control chromosomes in the GnomAD database, including 2,698 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 0.16 (2698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24602 AN: 151972 Hom.: 2696 Cov.: 31

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.162 AC: 24609 AN: 152090 Hom.: 2698 Cov.: 31 AF XY: 0.169 AC XY: 12537 AN XY: 74320

Gnomad4 AFR AF: 0.0359

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.149

Alfa AF: 0.184 Hom.: 5724

Bravo AF: 0.147

Asia WGS AF: 0.220 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.77
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11655550; hg19: chr17-37610123;