2-67052828-G-A

Variant names:

• chr2-67052828-G-A
• rs7594674
• ENST00000758901.1:n.365+10757G>A

Variant summary

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

The ENST00000758901.1(ENSG00000223859):​n.365+10757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 148,908 control chromosomes in the GnomAD database, including 38,295 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 0.72 (38295 hom., cov: 24)
• Consequence: ENSG00000223859 ENST00000758901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 2 publications found

Genes affected

ENSG00000223859 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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
ENSG00000223859	ENST00000758901.1	n.365+10757G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.716 AC: 106564 AN: 148822 Hom.: 38287 Cov.: 24

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.716 AC: 106612 AN: 148908 Hom.: 38295 Cov.: 24 AF XY: 0.714 AC XY: 51693 AN XY: 72448

African (AFR) AF: 0.737 AC: 29659 AN: 40256

American (AMR) AF: 0.667 AC: 9904 AN: 14856

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2541 AN: 3454

East Asian (EAS) AF: 0.824 AC: 4141 AN: 5028

South Asian (SAS) AF: 0.753 AC: 3531 AN: 4692

European-Finnish (FIN) AF: 0.649 AC: 6405 AN: 9872

Middle Eastern (MID) AF: 0.755 AC: 213 AN: 282

European-Non Finnish (NFE) AF: 0.712 AC: 48087 AN: 67514

Other (OTH) AF: 0.722 AC: 1482 AN: 2052

Alfa AF: 0.652 Hom.: 3349

Bravo AF: 0.715

Asia WGS AF: 0.773 AC: 2682 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.5
DANN	Benign	0.54
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs7594674; hg19: chr2-67279960;