18-31247414-T-C

Variant names:

• chr18-31247414-T-C
• rs7233386
• ENST00000715888.1:n.395-2910T>C

Variant summary

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

The ENST00000715888.1(DSCAS):​n.395-2910T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,098 control chromosomes in the GnomAD database, including 30,522 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 0.61 (30522 hom., cov: 32)
• Consequence: DSCAS ENST00000715888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 4 publications found

Genes affected

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

ENSG00000293651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372049	XR_001753388.2	n.100-2910T>C		intron_variant	Intron 1 of 3
LOC105372049	XR_935334.3	n.100-2910T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSCAS	ENST00000715888.1	n.395-2910T>C		intron_variant	Intron 4 of 4
ENSG00000293651	ENST00000716842.1	n.165-2910T>C		intron_variant	Intron 1 of 2
ENSG00000293651	ENST00000716843.1	n.92-2910T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93090 AN: 151980 Hom.: 30483 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.613 AC: 93182 AN: 152098 Hom.: 30522 Cov.: 32 AF XY: 0.614 AC XY: 45681 AN XY: 74344

African (AFR) AF: 0.813 AC: 33764 AN: 41512

American (AMR) AF: 0.421 AC: 6437 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1083 AN: 5182

South Asian (SAS) AF: 0.508 AC: 2447 AN: 4818

European-Finnish (FIN) AF: 0.738 AC: 7792 AN: 10564

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37928 AN: 67958

Other (OTH) AF: 0.586 AC: 1239 AN: 2116

Alfa AF: 0.567 Hom.: 63318

Bravo AF: 0.595

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.90
DANN	Benign	0.43
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs7233386; hg19: chr18-28827377;