15-25119648-C-T

Position:

• chr15-25119648-C-T

Variant summary

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

The NR_023915.1(IPW):​n.1670C>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 0.417 in 151,872 control chromosomes in the GnomAD database, including 13,502 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 0.42 (13502 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IPW NR_023915.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

Genes affected

SNHG14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IPW	NR_023915.1	n.1670C>T		non_coding_transcript_exon_variant	3/3
SNHG14	NR_146177.1	n.10396+1266C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG14	ENST00000626200.3	n.969C>T		non_coding_transcript_exon_variant	5/5	1
SNHG14	ENST00000549804.7	n.5016C>T		non_coding_transcript_exon_variant	33/33	5
SNHG14	ENST00000640631.2	n.12290C>T		non_coding_transcript_exon_variant	38/38	5

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63314 AN: 151754 Hom.: 13484 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.415

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.417 AC: 63357 AN: 151872 Hom.: 13502 Cov.: 32 AF XY: 0.420 AC XY: 31138 AN XY: 74208

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.417

Alfa AF: 0.415 Hom.: 18506

Bravo AF: 0.432

Asia WGS AF: 0.484 AC: 1682 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs691; hg19: chr15-25364795;