Variant rs1809319 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002035.4(KDSR):c.321+97A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 1,604,996 control chromosomes in the GnomAD database, including 336,579 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 0.62 ( 29252 hom., cov: 32)

Exomes 𝑓: 0.65 ( 307327 hom. )

Consequence

KDSR
NM_002035.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Variant links:

Genes affected

KDSR (HGNC:4021): (3-ketodihydrosphingosine reductase) The protein encoded by this gene catalyzes the reduction of 3-ketodihydrosphingosine to dihydrosphingosine. The putative active site residues of the encoded protein are found on the cytosolic side of the endoplasmic reticulum membrane. A chromosomal rearrangement involving this gene is a cause of follicular lymphoma, also known as type II chronic lymphatic leukemia. The mutation of a conserved residue in the bovine ortholog causes spinal muscular atrophy. [provided by RefSeq, Jul 2008]

KDSR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KDSR	NM_002035.4 linkuse as main transcript	c.321+97A>G		intron_variant		ENST00000645214.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KDSR	ENST00000645214.2 linkuse as main transcript	c.321+97A>G		intron_variant			NM_002035.4	P1	Q06136-1

Frequencies

GnomAD3 genomes

AF:

0.617

AC:

93804

AN:

151972

Hom.:

29243

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.667

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.601

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.658

Gnomad FIN

AF:

0.645

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.664

Gnomad OTH

AF:

0.624

GnomAD4 exome

AF:

0.649

AC:

943044

AN:

1452906

Hom.:

307327

Cov.:

AF XY:

0.650

AC XY:

469745

AN XY:

722508

show subpopulations

Gnomad4 AFR exome

AF:

0.538

Gnomad4 AMR exome

AF:

0.618

Gnomad4 ASJ exome

AF:

0.608

Gnomad4 EAS exome

AF:

0.481

Gnomad4 SAS exome

AF:

0.674

Gnomad4 FIN exome

AF:

0.660

Gnomad4 NFE exome

AF:

0.659

Gnomad4 OTH exome

AF:

0.632

GnomAD4 genome

AF:

0.617

AC:

93839

AN:

152090

Hom.:

29252

Cov.:

AF XY:

0.615

AC XY:

45728

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.540

Gnomad4 AMR

AF:

0.635

Gnomad4 ASJ

AF:

0.601

Gnomad4 EAS

AF:

0.469

Gnomad4 SAS

AF:

0.659

Gnomad4 FIN

AF:

0.645

Gnomad4 NFE

AF:

0.664

Gnomad4 OTH

AF:

0.619

Alfa

AF:

0.634

Hom.:

28215

Bravo

AF:

0.606

Asia WGS

AF:

0.548

AC:

1908

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

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.61

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.61

Position offset: 1

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over