2-175812356-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985962	XR_007087312.1	n.149+26534T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289349	ENST00000685522.2	n.464-20255A>G		intron_variant	Intron 1 of 2
ENSG00000289349	ENST00000692740.2	n.326-20255A>G		intron_variant	Intron 2 of 3
ENSG00000289349	ENST00000840653.1	n.272-20255A>G		intron_variant	Intron 2 of 3

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 v4.3

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;