chr20-18823379-G-C

Variant names:

• chr20-18823379-G-C
• rs6136524
• ENST00000623418.2:n.272+1887C>G

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+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 ENST00000623418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623418.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCP2D1-AS1	NR_161342.1		n.268+1887C>G		intron	N/A
	SCP2D1-AS1	NR_161343.1		n.244+1887C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCP2D1-AS1	ENST00000623418.2	TSL:2	n.272+1887C>G		intron	N/A
	SCP2D1-AS1	ENST00000730019.1		n.274+1887C>G		intron	N/A

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

African (AFR) AF: 0.155 AC: 6413 AN: 41444

American (AMR) AF: 0.343 AC: 5239 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3468

East Asian (EAS) AF: 0.594 AC: 3057 AN: 5146

South Asian (SAS) AF: 0.481 AC: 2309 AN: 4798

European-Finnish (FIN) AF: 0.423 AC: 4455 AN: 10540

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24175 AN: 67928

Other (OTH) AF: 0.322 AC: 679 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.26
PhyloP100		0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6136524;

hg19: chr20-18804023;