chr17-39453870-T-C

Variant names:

• chr17-39453870-T-C
• rs11655550

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;