chr17-39453870-T-C

Variant names:

• chr17-39453870-T-C
• rs11655550

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0359 AC: 1493 AN: 41556

American (AMR) AF: 0.195 AC: 2977 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5172

South Asian (SAS) AF: 0.213 AC: 1028 AN: 4816

European-Finnish (FIN) AF: 0.358 AC: 3774 AN: 10542

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13039 AN: 67980

Other (OTH) AF: 0.149 AC: 315 AN: 2110

Alfa AF: 0.178 Hom.: 8795

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
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs11655550; hg19: chr17-37610123;