rs8075776

Variant names:

• chr17-40998411-C-T
• rs8075776
• ENST00000815517.1:n.219+17804C>T

Variant summary

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

The ENST00000815517.1(ENSG00000306126):​n.219+17804C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,922 control chromosomes in the GnomAD database, including 9,106 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 0.29 (9106 hom., cov: 32)
• Consequence: ENSG00000306126 ENST00000815517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 1 publications found

Genes affected

ENSG00000306126 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 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
ENSG00000306126	ENST00000815517.1	n.219+17804C>T		intron_variant	Intron 2 of 2
ENSG00000306126	ENST00000815518.1	n.159+17804C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44579 AN: 151806 Hom.: 9073 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.294 AC: 44656 AN: 151922 Hom.: 9106 Cov.: 32 AF XY: 0.295 AC XY: 21908 AN XY: 74270

African (AFR) AF: 0.577 AC: 23883 AN: 41382

American (AMR) AF: 0.269 AC: 4108 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1424 AN: 5162

South Asian (SAS) AF: 0.285 AC: 1377 AN: 4824

European-Finnish (FIN) AF: 0.177 AC: 1861 AN: 10530

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10401 AN: 67966

Other (OTH) AF: 0.289 AC: 609 AN: 2110

Alfa AF: 0.347 Hom.: 2958

Bravo AF: 0.316

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	8.1
DANN	Benign	0.61
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs8075776; hg19: chr17-39154663;