rs10498025

Variant names:

• chr2-214884532-A-G
• rs10498025
• ENST00000607412.2:n.350+50427A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-214884532-A-G
• chr2-214884532-A-T

Variant summary

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

The ENST00000607412.2(SNHG31):​n.350+50427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,902 control chromosomes in the GnomAD database, including 3,642 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 0.21 (3642 hom., cov: 32)
• Consequence: SNHG31 ENST00000607412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 7 publications found

Genes affected

SNHG31 (HGNC:54196): (small nucleolar RNA host gene 31)

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 (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607412.2. 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
	SNHG31	NR_110292.1		n.321+50427A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG31	ENST00000607412.2	TSL:2	n.350+50427A>G		intron	N/A
	SNHG31	ENST00000655899.1		n.369+50427A>G		intron	N/A
	SNHG31	ENST00000664818.2		n.451+50427A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32552 AN: 151782 Hom.: 3644 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.214 AC: 32538 AN: 151902 Hom.: 3642 Cov.: 32 AF XY: 0.216 AC XY: 16012 AN XY: 74234

African (AFR) AF: 0.153 AC: 6361 AN: 41472

American (AMR) AF: 0.178 AC: 2714 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1125 AN: 5140

South Asian (SAS) AF: 0.345 AC: 1651 AN: 4792

European-Finnish (FIN) AF: 0.238 AC: 2513 AN: 10542

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16520 AN: 67906

Other (OTH) AF: 0.222 AC: 468 AN: 2106

Alfa AF: 0.225 Hom.: 2163

Bravo AF: 0.205

Asia WGS AF: 0.251 AC: 874 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	0.33
DANN	Benign	0.50
PhyloP100		-2.6

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: rs10498025;

hg19: chr2-215749256;