20-18820026-C-T

Variant names:

• chr20-18820026-C-T
• rs41526044
• ENST00000623418.2:n.272+5240G>A

Variant summary

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

The ENST00000623418.2(SCP2D1-AS1):​n.272+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 ENST00000623418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000623418.2	n.272+5240G>A		intron_variant	Intron 2 of 2	2
SCP2D1-AS1	ENST00000730019.1	n.274+5240G>A		intron_variant	Intron 2 of 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

African (AFR) AF: 0.0317 AC: 1315 AN: 41532

American (AMR) AF: 0.123 AC: 1883 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3472

East Asian (EAS) AF: 0.0515 AC: 266 AN: 5168

South Asian (SAS) AF: 0.106 AC: 509 AN: 4812

European-Finnish (FIN) AF: 0.147 AC: 1549 AN: 10568

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11379 AN: 68000

Other (OTH) AF: 0.115 AC: 244 AN: 2114

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs41526044; hg19: chr20-18800670;