rs202446

Positions:

• chr21-31656328-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449339.1(SOD1-DT):​n.399-901C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,942 control chromosomes in the GnomAD database, including 993 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 0.10 (993 hom., cov: 31)
• Consequence: SOD1-DT ENST00000449339.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.617

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOD1-DT	ENST00000449339.1	n.399-901C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15715 AN: 151822 Hom.: 992 Cov.: 31

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.103 AC: 15720 AN: 151942 Hom.: 993 Cov.: 31 AF XY: 0.100 AC XY: 7461 AN XY: 74260

Gnomad4 AFR AF: 0.0549

Gnomad4 AMR AF: 0.0986

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0146

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0917

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.126

Alfa AF: 0.125 Hom.: 177

Bravo AF: 0.100

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs202446; hg19: chr21-33028641;