rs2121283

Positions:

• chr2-214845614-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110292.1(SNHG31):​n.321+11509C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,102 control chromosomes in the GnomAD database, including 9,019 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 0.33 (9019 hom., cov: 33)
• Consequence: SNHG31 NR_110292.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNHG31	NR_110292.1	n.321+11509C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG31	ENST00000670391.1	n.437+2782C>T		intron_variant, non_coding_transcript_variant
SNHG31	ENST00000607412.1	n.321+11509C>T		intron_variant, non_coding_transcript_variant		2
SNHG31	ENST00000655899.1	n.369+11509C>T		intron_variant, non_coding_transcript_variant
SNHG31	ENST00000664818.1	n.333+11509C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50724 AN: 151982 Hom.: 9009 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.334 AC: 50757 AN: 152102 Hom.: 9019 Cov.: 33 AF XY: 0.338 AC XY: 25131 AN XY: 74328

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.335

Alfa AF: 0.369 Hom.: 5027

Bravo AF: 0.322

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2121283; hg19: chr2-215710338;