rs2739771

Positions:

• chr15-25201209-C-T

Variant summary

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

The ENST00000424333.6(SNHG14):​n.381C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 499,316 control chromosomes in the GnomAD database, including 125 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 0.025 (92 hom., cov: 33)
  • Exomes 𝑓: 0.0084 (33 hom.)
• Consequence: SNHG14 ENST00000424333.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

SNHG14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNHG14	NR_146177.1	n.13308C>T		non_coding_transcript_exon_variant	93/148

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG14	ENST00000424333.6	n.381C>T		non_coding_transcript_exon_variant	5/54	1
SNHG14	ENST00000424208.5	n.1931C>T		non_coding_transcript_exon_variant	21/34	5
SNHG14	ENST00000653489.1	n.295C>T		non_coding_transcript_exon_variant	4/59
SNHG14	ENST00000656420.1	n.850C>T		non_coding_transcript_exon_variant	7/57

Frequencies

GnomAD3 genomes AF: 0.0248 AC: 3780 AN: 152180 Hom.: 88 Cov.: 33

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00744

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00672

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.00842 AC: 2921 AN: 347018 Hom.: 33 Cov.: 0 AF XY: 0.00754 AC XY: 1507 AN XY: 199972

Gnomad4 AFR exome AF: 0.0674

Gnomad4 AMR exome AF: 0.00960

Gnomad4 ASJ exome AF: 0.0219

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00186

Gnomad4 FIN exome AF: 0.00726

Gnomad4 NFE exome AF: 0.00690

Gnomad4 OTH exome AF: 0.0137

GnomAD4 genome AF: 0.0250 AC: 3811 AN: 152298 Hom.: 92 Cov.: 33 AF XY: 0.0249 AC XY: 1851 AN XY: 74462

Gnomad4 AFR AF: 0.0689

Gnomad4 AMR AF: 0.0170

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.00744

Gnomad4 NFE AF: 0.00673

Gnomad4 OTH AF: 0.0203

Alfa AF: 0.0206 Hom.: 15

Bravo AF: 0.0266

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2739771; hg19: chr15-25446356;