rs282065

Variant names:

• chr6-90591645-G-A
• rs282065
• ENST00000762879.1:n.1207+810G>A

Variant summary

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

The ENST00000762879.1(ENSG00000299366):​n.1207+810G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151,930 control chromosomes in the GnomAD database, including 36,087 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 0.69 (36087 hom., cov: 31)
• Consequence: ENSG00000299366 ENST00000762879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 4 publications found

Genes affected

ENSG00000299366 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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
ENSG00000299366	ENST00000762879.1	n.1207+810G>A		intron_variant	Intron 3 of 3
ENSG00000299366	ENST00000762880.1	n.884+810G>A		intron_variant	Intron 3 of 3
ENSG00000299366	ENST00000762881.1	n.749+810G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104272 AN: 151814 Hom.: 36062 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.687 AC: 104345 AN: 151930 Hom.: 36087 Cov.: 31 AF XY: 0.681 AC XY: 50578 AN XY: 74234

African (AFR) AF: 0.709 AC: 29368 AN: 41406

American (AMR) AF: 0.633 AC: 9672 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2725 AN: 3468

East Asian (EAS) AF: 0.468 AC: 2413 AN: 5152

South Asian (SAS) AF: 0.689 AC: 3314 AN: 4812

European-Finnish (FIN) AF: 0.639 AC: 6736 AN: 10546

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47794 AN: 67964

Other (OTH) AF: 0.733 AC: 1547 AN: 2110

Alfa AF: 0.699 Hom.: 146259

Bravo AF: 0.684

Asia WGS AF: 0.633 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs282065; hg19: chr6-91301364; COSMIC: COSV65235352;