chr2-214859826-C-T

Position:

• chr2-214859826-C-T

Variant summary

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

The ENST00000607412.1(SNHG31):​n.321+25721C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,814 control chromosomes in the GnomAD database, including 11,162 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 0.37 (11162 hom., cov: 31)
• Consequence: SNHG31 ENST00000607412.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

Genes affected

SNHG31 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNHG31	NR_110292.1	n.321+25721C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG31	ENST00000607412.1	n.321+25721C>T		intron_variant		2
SNHG31	ENST00000655899.1	n.369+25721C>T		intron_variant
SNHG31	ENST00000664818.1	n.333+25721C>T		intron_variant
SNHG31	ENST00000670391.1	n.437+16994C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56811 AN: 151696 Hom.: 11152 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.374 AC: 56852 AN: 151814 Hom.: 11162 Cov.: 31 AF XY: 0.376 AC XY: 27889 AN XY: 74194

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.391

Alfa AF: 0.413 Hom.: 6234

Bravo AF: 0.365

Asia WGS AF: 0.376 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11677798; hg19: chr2-215724550;