rs12323635

Variant names:

• chr14-95159374-C-T
• rs12323635
• ENST00000435343.2:n.384+339C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435343.2(DICER1-AS1):​n.384+339C>T variant causes a intron 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 ENST00000435343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DICER1-AS1	NR_015415.1	n.373+339C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DICER1-AS1	ENST00000435343.2	n.384+339C>T		intron_variant	Intron 3 of 3	3
DICER1-AS1	ENST00000439819.8	n.403+339C>T		intron_variant	Intron 3 of 3	3
DICER1-AS1	ENST00000554631.2	n.1391+339C>T		intron_variant	Intron 1 of 2	2

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

African (AFR) AF: 0.721 AC: 29883 AN: 41424

American (AMR) AF: 0.425 AC: 6496 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2173 AN: 5164

South Asian (SAS) AF: 0.361 AC: 1733 AN: 4804

European-Finnish (FIN) AF: 0.401 AC: 4226 AN: 10526

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25985 AN: 67952

Other (OTH) AF: 0.479 AC: 1008 AN: 2106

Alfa AF: 0.427 Hom.: 6803

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
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs12323635; hg19: chr14-95625711;