21-31658867-C-T

Variant names:

• chr21-31658867-C-T
• rs17881274
• ENST00000449339.1:n.104+530G>A

Variant summary

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

The ENST00000449339.1(SOD1-DT):​n.104+530G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,230 control chromosomes in the GnomAD database, including 1,555 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 0.11 (1555 hom., cov: 33)
• Consequence: SOD1-DT ENST00000449339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449339.1. 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
	SOD1-DT	NR_187558.1		n.628+530G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOD1-DT	ENST00000449339.1	TSL:3	n.104+530G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16268 AN: 152112 Hom.: 1549 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0947

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.107 AC: 16307 AN: 152230 Hom.: 1555 Cov.: 33 AF XY: 0.106 AC XY: 7891 AN XY: 74438

African (AFR) AF: 0.263 AC: 10913 AN: 41504

American (AMR) AF: 0.0499 AC: 763 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.0118 AC: 57 AN: 4830

European-Finnish (FIN) AF: 0.0947 AC: 1005 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3276 AN: 68010

Other (OTH) AF: 0.0813 AC: 172 AN: 2116

Alfa AF: 0.0780 Hom.: 196

Bravo AF: 0.111

Asia WGS AF: 0.0250 AC: 87 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.68
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17881274; hg19: chr21-33031180;