15-24986947-T-A

Position:

• chr15-24986947-T-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000551312.6(ENSG00000214265):​n.*953+4510T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00302 in 519,188 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0030 (8 hom., cov: 33)
  • Exomes 𝑓: 0.0030 (2 hom.)
• Consequence: ENSG00000214265 ENST00000551312.6 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.594

Genes affected

SNHG14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNORD108	NR_001292.2	n.23T>A		non_coding_transcript_exon_variant	1/1
PWAR5	NR_022008.1	n.2088T>A		non_coding_transcript_exon_variant	1/1
SNHG14	NR_146177.1	n.3624+4510T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000214265	ENST00000551312.6	n.*953+4510T>A		intron_variant		5		ENSP00000451421.1

Frequencies

GnomAD3 genomes AF: 0.00303 AC: 461 AN: 152174 Hom.: 8 Cov.: 33

Gnomad AFR AF: 0.000531

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.000785

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00169

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00450

Gnomad OTH AF: 0.00383

GnomAD3 exomes AF: 0.00258 AC: 598 AN: 231822 Hom.: 1 AF XY: 0.00274 AC XY: 351 AN XY: 127908

Gnomad AFR exome AF: 0.000502

Gnomad AMR exome AF: 0.00137

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000462

Gnomad FIN exome AF: 0.00163

Gnomad NFE exome AF: 0.00459

Gnomad OTH exome AF: 0.00238

GnomAD4 exome AF: 0.00303 AC: 1110 AN: 366896 Hom.: 2 Cov.: 0 AF XY: 0.00290 AC XY: 611 AN XY: 210378

Gnomad4 AFR exome AF: 0.000476

Gnomad4 AMR exome AF: 0.00138

Gnomad4 ASJ exome AF: 0.0000851

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000524

Gnomad4 FIN exome AF: 0.00218

Gnomad4 NFE exome AF: 0.00488

Gnomad4 OTH exome AF: 0.00259

GnomAD4 genome AF: 0.00302 AC: 460 AN: 152292 Hom.: 8 Cov.: 33 AF XY: 0.00271 AC XY: 202 AN XY: 74470

Gnomad4 AFR AF: 0.000529

Gnomad4 AMR AF: 0.000784

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00169

Gnomad4 NFE AF: 0.00450

Gnomad4 OTH AF: 0.00379

Alfa AF: 0.00380 Hom.: 1

Bravo AF: 0.00299

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.79
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs188270533; hg19: chr15-25232094;