rs10498026

Variant names:

• chr2-214884626-G-A
• rs10498026
• ENST00000607412.2:n.350+50521G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-214884626-G-A
• chr2-214884626-G-C
• chr2-214884626-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000607412.2(SNHG31):​n.350+50521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,624 control chromosomes in the GnomAD database, including 15,506 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 0.45 (15506 hom., cov: 31)
• Consequence: SNHG31 ENST00000607412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNHG31	NR_110292.1	n.321+50521G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNHG31	ENST00000607412.2	n.350+50521G>A		intron_variant	Intron 2 of 3	2
SNHG31	ENST00000655899.1	n.369+50521G>A		intron_variant	Intron 2 of 3
SNHG31	ENST00000664818.2	n.451+50521G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67687 AN: 151504 Hom.: 15486 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.447 AC: 67738 AN: 151624 Hom.: 15506 Cov.: 31 AF XY: 0.448 AC XY: 33184 AN XY: 74072

African (AFR) AF: 0.361 AC: 14878 AN: 41258

American (AMR) AF: 0.518 AC: 7901 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1813 AN: 3468

East Asian (EAS) AF: 0.366 AC: 1883 AN: 5148

South Asian (SAS) AF: 0.453 AC: 2172 AN: 4796

European-Finnish (FIN) AF: 0.484 AC: 5062 AN: 10460

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32547 AN: 67928

Other (OTH) AF: 0.455 AC: 960 AN: 2112

Alfa AF: 0.473 Hom.: 8933

Bravo AF: 0.441

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	17
DANN	Benign	0.55
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10498026; hg19: chr2-215749350;