17-17619630-T-C

Variant names:

• chr17-17619630-T-C
• rs8081810
• ENST00000816800.1:n.204-7058T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000816800.1(ENSG00000264666):​n.204-7058T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000264666 ENST00000816800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 3 publications found

Genes affected

ENSG00000264666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264666	ENST00000816800.1	n.204-7058T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.397 AC: 16437 AN: 41412

American (AMR) AF: 0.249 AC: 3800 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1766 AN: 5150

South Asian (SAS) AF: 0.161 AC: 777 AN: 4816

European-Finnish (FIN) AF: 0.145 AC: 1532 AN: 10582

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10344 AN: 67990

Other (OTH) AF: 0.231 AC: 487 AN: 2112

Alfa AF: 0.176 Hom.: 1513

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs8081810; hg19: chr17-17522944;