rs1288097

Positions:

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

Variant summary

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

The NR_146394.1(SORD2P):​n.216+1179C>T 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 0.325 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_146394.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SORD2P	NR_146394.1	n.216+1179C>T		intron_variant, non_coding_transcript_variant
SORD2P	NR_146393.1	n.447+1179C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SORD2P	ENST00000558556.5	n.100+1179C>T		intron_variant, non_coding_transcript_variant
SORD2P	ENST00000561384.3	n.216+1179C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.0857

Gnomad4 NFE AF: 0.0877

Gnomad4 OTH AF: 0.276

Alfa AF: 0.129 Hom.: 1675

Bravo AF: 0.364

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1288097; hg19: chr15-45141373;