rs202447

Positions:

• chr21-31657061-C-A
• chr21-31657061-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000449339.1(SOD1-DT):​n.398+873G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00604 in 152,312 control chromosomes in the GnomAD database, including 5 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 0.0060 (5 hom., cov: 32)
• Consequence: SOD1-DT ENST00000449339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOD1-DT	NR_187558.1	n.790+873G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOD1-DT	ENST00000449339.1	n.398+873G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00604 AC: 920 AN: 152194 Hom.: 5 Cov.: 32

Gnomad AFR AF: 0.00154

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.00157

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.00452

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.00287

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

GnomAD4 genome AF: 0.00604 AC: 920 AN: 152312 Hom.: 5 Cov.: 32 AF XY: 0.00532 AC XY: 396 AN XY: 74486

Gnomad4 AFR AF: 0.00154

Gnomad4 AMR AF: 0.00157

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00452

Gnomad4 NFE AF: 0.0103

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00613 Hom.: 1

Bravo AF: 0.00559

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs202447; hg19: chr21-33029374;