rs2592232

Variant names:

• chr2-214861027-G-A
• rs2592232
• ENST00000607412.2:n.350+26922G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-214861027-G-A
• chr2-214861027-G-C
• chr2-214861027-G-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+26922G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 151,918 control chromosomes in the GnomAD database, including 41,473 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 (41473 hom., cov: 30)
• Consequence: SNHG31 ENST00000607412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG31	NR_110292.1		n.321+26922G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG31	ENST00000607412.2	TSL:2	n.350+26922G>A		intron	N/A
	SNHG31	ENST00000655899.1		n.369+26922G>A		intron	N/A
	SNHG31	ENST00000664818.2		n.451+26922G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111748 AN: 151798 Hom.: 41412 Cov.: 30

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.736 AC: 111872 AN: 151918 Hom.: 41473 Cov.: 30 AF XY: 0.735 AC XY: 54557 AN XY: 74204

African (AFR) AF: 0.817 AC: 33859 AN: 41438

American (AMR) AF: 0.760 AC: 11590 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2484 AN: 3470

East Asian (EAS) AF: 0.782 AC: 4033 AN: 5160

South Asian (SAS) AF: 0.648 AC: 3111 AN: 4802

European-Finnish (FIN) AF: 0.687 AC: 7240 AN: 10538

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47379 AN: 67942

Other (OTH) AF: 0.709 AC: 1496 AN: 2110

Alfa AF: 0.707 Hom.: 19264

Bravo AF: 0.746

Asia WGS AF: 0.735 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.29
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2592232; hg19: chr2-215725751;