17-17619630-T-C

Position:

• chr17-17619630-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 0.238 in 151,976 control chromosomes in the GnomAD database, including 5,227 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 0.24 (5227 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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: 0.238 AC: 36082 AN: 151858 Hom.: 5216 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.238 AC: 36131 AN: 151976 Hom.: 5227 Cov.: 31 AF XY: 0.237 AC XY: 17599 AN XY: 74292

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.231

Alfa AF: 0.174 Hom.: 1334

Bravo AF: 0.257

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8081810; hg19: chr17-17522944;