rs6575501

Variant names:

• chr14-95173992-C-A
• rs6575501
• ENST00000435343.2:n.385-5512C>A

Variant summary

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

The ENST00000435343.2(DICER1-AS1):​n.385-5512C>A variant causes a intron 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 ENST00000435343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 2 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=-0.89).
• 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 rank	MANE	Protein	UniProt
DICER1-AS1	NR_015415.1	n.374-5512C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DICER1-AS1	ENST00000435343.2	n.385-5512C>A		intron_variant	Intron 3 of 3	3
DICER1-AS1	ENST00000439819.8	n.404-5507C>A		intron_variant	Intron 3 of 3	3
DICER1-AS1	ENST00000554631.2	n.1392-5507C>A		intron_variant	Intron 1 of 2	2

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

African (AFR) AF: 0.116 AC: 4818 AN: 41556

American (AMR) AF: 0.0395 AC: 605 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0764 AC: 265 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5192

South Asian (SAS) AF: 0.0153 AC: 74 AN: 4830

European-Finnish (FIN) AF: 0.0457 AC: 485 AN: 10608

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0526 AC: 3579 AN: 68020

Other (OTH) AF: 0.0624 AC: 132 AN: 2114

Alfa AF: 0.0618 Hom.: 664

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
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs6575501; hg19: chr14-95640329;