rs726032

Variant names:

• chr2-175792369-G-A
• rs726032
• ENST00000685522.2:n.464-40242G>A

Variant summary

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

The ENST00000685522.2(ENSG00000289349):​n.464-40242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,078 control chromosomes in the GnomAD database, including 3,788 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 0.22 (3788 hom., cov: 32)
• Consequence: ENSG00000289349 ENST00000685522.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588
• Publications: 4 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=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985962	XR_007087312.1	n.150-6593C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289349	ENST00000685522.2	n.464-40242G>A		intron_variant	Intron 1 of 2
ENSG00000289349	ENST00000692740.2	n.326-40242G>A		intron_variant	Intron 2 of 3
ENSG00000289349	ENST00000840653.1	n.272-40242G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33293 AN: 151960 Hom.: 3782 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.219 AC: 33327 AN: 152078 Hom.: 3788 Cov.: 32 AF XY: 0.224 AC XY: 16633 AN XY: 74330

African (AFR) AF: 0.206 AC: 8536 AN: 41508

American (AMR) AF: 0.186 AC: 2846 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3472

East Asian (EAS) AF: 0.161 AC: 832 AN: 5164

South Asian (SAS) AF: 0.337 AC: 1623 AN: 4818

European-Finnish (FIN) AF: 0.274 AC: 2889 AN: 10552

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15089 AN: 67974

Other (OTH) AF: 0.235 AC: 496 AN: 2108

Alfa AF: 0.224 Hom.: 6613

Bravo AF: 0.212

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	14
DANN	Benign	0.62
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs726032; hg19: chr2-176657097;