ENST00000715888.1:n.394+2820T>C

Variant names:

• chr18-31209762-T-C
• rs2920001
• ENST00000715888.1:n.394+2820T>C

Variant summary

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

The ENST00000715888.1(DSCAS):​n.394+2820T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,088 control chromosomes in the GnomAD database, including 3,195 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 0.20 (3195 hom., cov: 32)
• Consequence: DSCAS ENST00000715888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 6 publications found

Genes affected

DSCAS (HGNC:51116): (DSC1/DSC2 antisense RNA)

ENSG00000310241 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSCAS	ENST00000715888.1	n.394+2820T>C		intron_variant	Intron 4 of 4
ENSG00000310241	ENST00000848515.1	n.158-2804A>G		intron_variant	Intron 1 of 1
ENSG00000310241	ENST00000848516.1	n.45-1606A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29750 AN: 151970 Hom.: 3185 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.196 AC: 29793 AN: 152088 Hom.: 3195 Cov.: 32 AF XY: 0.194 AC XY: 14422 AN XY: 74360

African (AFR) AF: 0.277 AC: 11473 AN: 41436

American (AMR) AF: 0.148 AC: 2255 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3466

East Asian (EAS) AF: 0.114 AC: 592 AN: 5182

South Asian (SAS) AF: 0.124 AC: 599 AN: 4826

European-Finnish (FIN) AF: 0.202 AC: 2143 AN: 10598

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11642 AN: 67988

Other (OTH) AF: 0.184 AC: 388 AN: 2114

Alfa AF: 0.177 Hom.: 8749

Bravo AF: 0.196

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.069
DANN	Benign	0.42
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2920001; hg19: chr18-28789725;