chr8-2216912-T-C

Variant names:

• chr8-2216912-T-C
• rs1382608
• ENST00000776947.1:n.213-9518T>C

Variant summary

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

The ENST00000776947.1(ENSG00000288782):​n.213-9518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,966 control chromosomes in the GnomAD database, including 25,751 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 0.56 (25751 hom., cov: 32)
• Consequence: ENSG00000288782 ENST00000776947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 4 publications found

Genes affected

ENSG00000288782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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
ENSG00000288782	ENST00000776947.1	n.213-9518T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84554 AN: 151848 Hom.: 25704 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.557 AC: 84657 AN: 151966 Hom.: 25751 Cov.: 32 AF XY: 0.548 AC XY: 40724 AN XY: 74276

African (AFR) AF: 0.812 AC: 33656 AN: 41464

American (AMR) AF: 0.454 AC: 6942 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1468 AN: 3448

East Asian (EAS) AF: 0.409 AC: 2106 AN: 5148

South Asian (SAS) AF: 0.292 AC: 1406 AN: 4812

European-Finnish (FIN) AF: 0.451 AC: 4765 AN: 10570

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32677 AN: 67936

Other (OTH) AF: 0.514 AC: 1084 AN: 2108

Alfa AF: 0.492 Hom.: 18336

Bravo AF: 0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1382608; hg19: chr8-2164581;