rs10182181

Variant names:

• chr2-24927427-A-G
• rs10182181
• ENST00000841804.1:n.189+3224A>G

Variant summary

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

The ENST00000841804.1(ENSG00000309511):​n.189+3224A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,106 control chromosomes in the GnomAD database, including 26,437 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 0.56 (26437 hom., cov: 32)
• Consequence: ENSG00000309511 ENST00000841804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 146 publications found

Genes affected

ENSG00000309511 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841804.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309511	ENST00000841804.1		n.189+3224A>G		intron	N/A
	ENSG00000309570	ENST00000842089.1		n.-202T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85092 AN: 151988 Hom.: 26377 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.560 AC: 85207 AN: 152106 Hom.: 26437 Cov.: 32 AF XY: 0.550 AC XY: 40874 AN XY: 74338

African (AFR) AF: 0.844 AC: 35042 AN: 41524

American (AMR) AF: 0.402 AC: 6150 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2242 AN: 5156

South Asian (SAS) AF: 0.480 AC: 2313 AN: 4814

European-Finnish (FIN) AF: 0.403 AC: 4253 AN: 10566

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32244 AN: 67978

Other (OTH) AF: 0.521 AC: 1099 AN: 2108

Alfa AF: 0.497 Hom.: 45582

Bravo AF: 0.570

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.6
DANN	Benign	0.72
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10182181;

hg19: chr2-25150296;