rs1288097

Variant names:

• chr15-44849175-G-A
• rs1288097
• ENST00000558556.5:n.100+1179C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-44849175-G-A
• chr15-44849175-G-C

Variant summary

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

The NR_146393.1(SORD2P):​n.447+1179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,032 control chromosomes in the GnomAD database, including 15,876 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 0.33 (15876 hom., cov: 31)
• Consequence: SORD2P NR_146393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667
• Publications: 2 publications found

Genes affected

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

SORD2P (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_146393.1. 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
	SORD2P	NR_146393.1		n.447+1179C>T		intron	N/A
	SORD2P	NR_146394.1		n.216+1179C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SORD2P	ENST00000558556.5	TSL:6	n.100+1179C>T		intron	N/A
	SORD2P	ENST00000561384.3	TSL:5	n.216+1179C>T		intron	N/A
	SORD2P	ENST00000737492.1		n.97+1179C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49305 AN: 151914 Hom.: 15794 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0877

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.325 AC: 49467 AN: 152032 Hom.: 15876 Cov.: 31 AF XY: 0.322 AC XY: 23918 AN XY: 74360

African (AFR) AF: 0.824 AC: 34089 AN: 41392

American (AMR) AF: 0.278 AC: 4252 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3466

East Asian (EAS) AF: 0.412 AC: 2132 AN: 5174

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4822

European-Finnish (FIN) AF: 0.0857 AC: 909 AN: 10604

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.0877 AC: 5965 AN: 67986

Other (OTH) AF: 0.276 AC: 583 AN: 2110

Alfa AF: 0.199 Hom.: 7581

Bravo AF: 0.364

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.47
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1288097; hg19: chr15-45141373;