chr15-25278417-C-T

Position:

• chr15-25278417-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NR_146177.1(SNHG14):​n.18355-430C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00369 in 518,356 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0053 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0030 (4 hom.)
• Consequence: SNHG14 NR_146177.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.123

Genes affected

SNHG14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 15-25278417-C-T is Benign according to our data. Variant chr15-25278417-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2498602.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNHG14	NR_146177.1	n.18355-430C>T		intron_variant
SNORD109B	NR_001289.1	n.*8C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG14	ENST00000424333.6	n.5729-430C>T		intron_variant		1
SNHG14	ENST00000554726.2	n.447-426C>T		intron_variant		1
SNHG14	ENST00000452731.5	n.841-430C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00527 AC: 802 AN: 152066 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00747

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.00483

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00193

Gnomad OTH AF: 0.00624

GnomAD3 exomes AF: 0.00329 AC: 753 AN: 228852 Hom.: 1 AF XY: 0.00287 AC XY: 363 AN XY: 126520

Gnomad AFR exome AF: 0.00664

Gnomad AMR exome AF: 0.00837

Gnomad ASJ exome AF: 0.00531

Gnomad EAS exome AF: 0.00370

Gnomad SAS exome AF: 0.00265

Gnomad FIN exome AF: 0.00232

Gnomad NFE exome AF: 0.00118

Gnomad OTH exome AF: 0.00461

GnomAD4 exome AF: 0.00303 AC: 1109 AN: 366172 Hom.: 4 Cov.: 0 AF XY: 0.00278 AC XY: 584 AN XY: 209966

Gnomad4 AFR exome AF: 0.00658

Gnomad4 AMR exome AF: 0.00845

Gnomad4 ASJ exome AF: 0.00607

Gnomad4 EAS exome AF: 0.00373

Gnomad4 SAS exome AF: 0.00335

Gnomad4 FIN exome AF: 0.00343

Gnomad4 NFE exome AF: 0.00141

Gnomad4 OTH exome AF: 0.00343

GnomAD4 genome AF: 0.00530 AC: 806 AN: 152184 Hom.: 2 Cov.: 32 AF XY: 0.00534 AC XY: 397 AN XY: 74404

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.00746

Gnomad4 ASJ AF: 0.00923

Gnomad4 EAS AF: 0.00504

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.00396

Gnomad4 NFE AF: 0.00193

Gnomad4 OTH AF: 0.00617

Alfa AF: 0.00126 Hom.: 0

Bravo AF: 0.00602

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2024

SNHG14: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs142202250; hg19: chr15-25523564;