20-18823379-G-C

Position:

• chr20-18823379-G-C

Variant summary

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

The ENST00000623418.1(SCP2D1-AS1):​n.218+1887C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,892 control chromosomes in the GnomAD database, including 8,375 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 0.31 (8375 hom., cov: 31)
• Consequence: SCP2D1-AS1 ENST00000623418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

Genes affected

SCP2D1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCP2D1-AS1	NR_161342.1	n.268+1887C>G		intron_variant
SCP2D1-AS1	NR_161343.1	n.244+1887C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCP2D1-AS1	ENST00000623418.1	n.218+1887C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47579 AN: 151772 Hom.: 8377 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.313 AC: 47603 AN: 151892 Hom.: 8375 Cov.: 31 AF XY: 0.322 AC XY: 23872 AN XY: 74224

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.322

Alfa AF: 0.324 Hom.: 1027

Bravo AF: 0.300

Asia WGS AF: 0.516 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6136524; hg19: chr20-18804023;