rs735480

chr15-44860173-T-C

Variant summary

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

The NR_146394.1(SORD2P):n.183-9786A>G 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 0.343 in 152,116 control chromosomes in the GnomAD database, including 16,213 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 0.34 (16213 hom., cov: 32)
• Consequence: SORD2P NR_146394.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

SORD2P (HGNC:49919): (sorbitol dehydrogenase 2, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SORD2P	NR_146394.1	n.183-9786A>G		intron_variant, non_coding_transcript_variant
SORD2P	NR_146393.1	n.414-9786A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SORD2P	ENST00000558556.5	n.66+1612A>G		intron_variant, non_coding_transcript_variant
SORD2P	ENST00000561384.3	n.183-9786A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51960 AN: 151998 Hom.: 16130 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.343 AC: 52124 AN: 152116 Hom.: 16213 Cov.: 32 AF XY: 0.340 AC XY: 25269 AN XY: 74378

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.290

Alfa AF: 0.183 Hom.: 3501

Bravo AF: 0.376

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.098
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735480; hg19: chr15-45152371;