chr2-175812356-A-G

Variant names:

• chr2-175812356-A-G
• rs1446829
• ENST00000685522.2:n.464-20255A>G

Variant summary

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

The ENST00000685522.2(ENSG00000289349):​n.464-20255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,238 control chromosomes in the GnomAD database, including 41,920 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 0.74 (41920 hom., cov: 33)
• Consequence: ENSG00000289349 ENST00000685522.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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.464-20255A>G		intron	N/A
	ENSG00000289349	ENST00000692740.2		n.326-20255A>G		intron	N/A
	ENSG00000289349	ENST00000840653.1		n.272-20255A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111857 AN: 152120 Hom.: 41871 Cov.: 33

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.735 AC: 111963 AN: 152238 Hom.: 41920 Cov.: 33 AF XY: 0.736 AC XY: 54765 AN XY: 74428

African (AFR) AF: 0.887 AC: 36839 AN: 41550

American (AMR) AF: 0.686 AC: 10506 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2209 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3737 AN: 5182

South Asian (SAS) AF: 0.735 AC: 3542 AN: 4822

European-Finnish (FIN) AF: 0.689 AC: 7301 AN: 10598

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

European-Non Finnish (NFE) AF: 0.671 AC: 45637 AN: 67994

Other (OTH) AF: 0.712 AC: 1502 AN: 2110

Alfa AF: 0.688 Hom.: 144148

Bravo AF: 0.739

Asia WGS AF: 0.774 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.82
DANN	Benign	0.51
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1446829; hg19: chr2-176677084;