rs6575501

Positions:

• chr14-95173992-C-A

Variant summary

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

The NR_015415.1(DICER1-AS1):​n.374-5512C>A 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 0.0663 in 152,296 control chromosomes in the GnomAD database, including 423 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 0.066 (423 hom., cov: 32)
• Consequence: DICER1-AS1 NR_015415.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DICER1-AS1	NR_015415.1	n.374-5512C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DICER1-AS1	ENST00000671073.2	n.1388-5507C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0662 AC: 10076 AN: 152178 Hom.: 420 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0663 AC: 10093 AN: 152296 Hom.: 423 Cov.: 32 AF XY: 0.0645 AC XY: 4805 AN XY: 74484

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.0457

Gnomad4 NFE AF: 0.0526

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0571 Hom.: 390

Bravo AF: 0.0685

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6575501; hg19: chr14-95640329;