14-95159374-C-T

Position:

• chr14-95159374-C-T

Variant summary

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

The NR_015415.1(DICER1-AS1):​n.373+339C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,920 control chromosomes in the GnomAD database, including 19,518 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 0.48 (19518 hom., cov: 31)
• Consequence: DICER1-AS1 NR_015415.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

Genes affected

DICER1-AS1 (HGNC:43017): (DICER1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DICER1-AS1	NR_015415.1	n.373+339C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DICER1-AS1	ENST00000671073.2	n.1387+339C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73383 AN: 151802 Hom.: 19475 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.484 AC: 73490 AN: 151920 Hom.: 19518 Cov.: 31 AF XY: 0.481 AC XY: 35679 AN XY: 74214

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.479

Alfa AF: 0.422 Hom.: 5566

Bravo AF: 0.494

Asia WGS AF: 0.432 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.95
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12323635; hg19: chr14-95625711;