2-175790010-A-G

Variant names:

• chr2-175790010-A-G
• rs7566934
• ENST00000685522.2:n.464-42601A>G

Variant summary

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

The ENST00000685522.2(ENSG00000289349):​n.464-42601A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,144 control chromosomes in the GnomAD database, including 40,571 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 0.73 (40571 hom., cov: 33)
• Consequence: ENSG00000289349 ENST00000685522.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 8 publications found

Genes affected

ENSG00000289349 (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 = 0.842 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685522.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289349	ENST00000685522.2		n.464-42601A>G		intron	N/A
	ENSG00000289349	ENST00000692740.2		n.326-42601A>G		intron	N/A
	ENSG00000289349	ENST00000840653.1		n.272-42601A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110228 AN: 152026 Hom.: 40524 Cov.: 33

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.725 AC: 110329 AN: 152144 Hom.: 40571 Cov.: 33 AF XY: 0.729 AC XY: 54196 AN XY: 74380

African (AFR) AF: 0.849 AC: 35245 AN: 41510

American (AMR) AF: 0.682 AC: 10414 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2154 AN: 3468

East Asian (EAS) AF: 0.804 AC: 4163 AN: 5176

South Asian (SAS) AF: 0.719 AC: 3472 AN: 4826

European-Finnish (FIN) AF: 0.729 AC: 7722 AN: 10598

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.662 AC: 44995 AN: 67976

Other (OTH) AF: 0.695 AC: 1467 AN: 2110

Alfa AF: 0.682 Hom.: 118694

Bravo AF: 0.727

Asia WGS AF: 0.796 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.37
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs7566934; hg19: chr2-176654738;