rs726033

Variant names:

• chr2-175792525-C-A
• rs726033
• ENST00000685522.2:n.464-40086C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-175792525-C-A
• chr2-175792525-C-T

Variant summary

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

The ENST00000685522.2(ENSG00000289349):​n.464-40086C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,130 control chromosomes in the GnomAD database, including 7,181 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 0.30 (7181 hom., cov: 33)
• Consequence: ENSG00000289349 ENST00000685522.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985962	XR_007087312.1	n.150-6749G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289349	ENST00000685522.2	n.464-40086C>A		intron_variant	Intron 1 of 2
ENSG00000289349	ENST00000692740.2	n.326-40086C>A		intron_variant	Intron 2 of 3
ENSG00000289349	ENST00000840653.1	n.272-40086C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45442 AN: 152012 Hom.: 7163 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.299 AC: 45515 AN: 152130 Hom.: 7181 Cov.: 33 AF XY: 0.301 AC XY: 22392 AN XY: 74364

African (AFR) AF: 0.394 AC: 16343 AN: 41486

American (AMR) AF: 0.218 AC: 3340 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 973 AN: 3470

East Asian (EAS) AF: 0.323 AC: 1673 AN: 5186

South Asian (SAS) AF: 0.393 AC: 1896 AN: 4828

European-Finnish (FIN) AF: 0.300 AC: 3176 AN: 10570

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17306 AN: 67978

Other (OTH) AF: 0.307 AC: 649 AN: 2114

Alfa AF: 0.171 Hom.: 356

Bravo AF: 0.299

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.21
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs726033; hg19: chr2-176657253;