chr21-31649707-T-C

Variant names:

• chr21-31649707-T-C
• rs2173962
• ENST00000752262.1:n.360+5567A>G

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+5567A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 152,028 control chromosomes in the GnomAD database, including 508 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 0.070 (508 hom., cov: 31)
• Consequence: SOD1-DT ENST00000752262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 7 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=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752262.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOD1-DT	ENST00000752262.1		n.360+5567A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0703 AC: 10676 AN: 151910 Hom.: 501 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0952

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0705 AC: 10715 AN: 152028 Hom.: 508 Cov.: 31 AF XY: 0.0713 AC XY: 5295 AN XY: 74284

African (AFR) AF: 0.137 AC: 5675 AN: 41446

American (AMR) AF: 0.0344 AC: 525 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5180

South Asian (SAS) AF: 0.0110 AC: 53 AN: 4820

European-Finnish (FIN) AF: 0.0952 AC: 1003 AN: 10538

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3231 AN: 67986

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0667 Hom.: 88

Bravo AF: 0.0687

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.96
PhyloP100		0.11

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: rs2173962;

hg19: chr21-33022020;