17-42615670-C-T

Variant names:

• chr17-42615670-C-T
• rs9911799
• ENST00000766605.1:n.*210G>A

Variant summary

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

The ENST00000766605.1(ENSG00000299802):​n.*210G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,922 control chromosomes in the GnomAD database, including 19,800 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 0.51 (19800 hom., cov: 31)
• Consequence: ENSG00000299802 ENST00000766605.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 12 publications found

Genes affected

ENSG00000299802 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 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
ENSG00000299802	ENST00000766605.1	n.*210G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77102 AN: 151804 Hom.: 19775 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.508 AC: 77167 AN: 151922 Hom.: 19800 Cov.: 31 AF XY: 0.506 AC XY: 37593 AN XY: 74248

African (AFR) AF: 0.450 AC: 18652 AN: 41408

American (AMR) AF: 0.477 AC: 7278 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2358 AN: 5160

South Asian (SAS) AF: 0.645 AC: 3097 AN: 4802

European-Finnish (FIN) AF: 0.531 AC: 5609 AN: 10562

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37265 AN: 67952

Other (OTH) AF: 0.481 AC: 1016 AN: 2112

Alfa AF: 0.506 Hom.: 2922

Bravo AF: 0.496

Asia WGS AF: 0.581 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.58
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9911799; hg19: chr17-40767688;