21-31653354-C-T

Variant names:

• chr21-31653354-C-T
• rs202445
• ENST00000752262.1:n.360+1920G>A

Variant summary

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

The ENST00000752262.1(SOD1-DT):​n.360+1920G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,066 control chromosomes in the GnomAD database, including 56,354 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 0.86 (56354 hom., cov: 30)
• Consequence: SOD1-DT ENST00000752262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 15 publications found

Genes affected

SOD1-DT (HGNC:55683): (SOD1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOD1-DT	NR_187558.1	n.*233G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOD1-DT	ENST00000752262.1	n.360+1920G>A		intron_variant	Intron 2 of 2
SOD1-DT	ENST00000449339.1	n.*239G>A		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130495 AN: 151948 Hom.: 56299 Cov.: 30

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.859 AC: 130605 AN: 152066 Hom.: 56354 Cov.: 30 AF XY: 0.858 AC XY: 63770 AN XY: 74306

African (AFR) AF: 0.928 AC: 38501 AN: 41506

American (AMR) AF: 0.849 AC: 12958 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3024 AN: 3468

East Asian (EAS) AF: 0.990 AC: 5123 AN: 5176

South Asian (SAS) AF: 0.840 AC: 4051 AN: 4824

European-Finnish (FIN) AF: 0.805 AC: 8469 AN: 10522

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55637 AN: 68002

Other (OTH) AF: 0.848 AC: 1786 AN: 2106

Alfa AF: 0.842 Hom.: 27281

Bravo AF: 0.865

Asia WGS AF: 0.915 AC: 3184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs202445; hg19: chr21-33025667;