20-18820026-C-T

Variant names:

• chr20-18820026-C-T
• rs41526044
• ENST00000623418.1:n.218+5240G>A

Variant summary

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

The ENST00000623418.1(SCP2D1-AS1):​n.218+5240G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,160 control chromosomes in the GnomAD database, including 1,309 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 0.12 (1309 hom., cov: 32)
• Consequence: SCP2D1-AS1 ENST00000623418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

SCP2D1-AS1 (HGNC:16210): (SCP2D1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCP2D1-AS1	NR_161342.1	n.268+5240G>A		intron_variant	Intron 2 of 2
SCP2D1-AS1	NR_161343.1	n.244+5240G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCP2D1-AS1	ENST00000623418.1	n.218+5240G>A		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17781 AN: 152042 Hom.: 1308 Cov.: 32

Gnomad AFR AF: 0.0318

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.117 AC: 17782 AN: 152160 Hom.: 1309 Cov.: 32 AF XY: 0.115 AC XY: 8541 AN XY: 74366

Gnomad4 AFR AF: 0.0317

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0515

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0949 Hom.: 199

Bravo AF: 0.111

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.3
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41526044; hg19: chr20-18800670;