chr18-63367187-T-C

Variant names:

• chr18-63367187-T-C
• rs402348
• NM_002035.4:c.-69A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002035.4(KDSR):​c.-69A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KDSR NM_002035.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 15 publications found

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-DT (HGNC:55299): (KDSR divergent transcript)

LOC124904317 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002035.4. 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
	KDSR	NM_002035.4	MANE Select	c.-69A>G		5_prime_UTR	Exon 1 of 10	NP_002026.1	Q06136-1
	KDSR-DT	NR_186602.1		n.-137T>C		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KDSR	ENST00000645214.2	MANE Select	c.-69A>G		5_prime_UTR	Exon 1 of 10	ENSP00000494352.1	Q06136-1
	KDSR	ENST00000951441.1		c.-69A>G		5_prime_UTR	Exon 1 of 11	ENSP00000621500.1
	KDSR	ENST00000882920.1		c.-69A>G		5_prime_UTR	Exon 1 of 10	ENSP00000552979.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 634550 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 307862

African (AFR) AF: 0.00 AC: 0 AN: 12776

American (AMR) AF: 0.00 AC: 0 AN: 6796

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10120

East Asian (EAS) AF: 0.00 AC: 0 AN: 21884

South Asian (SAS) AF: 0.00 AC: 0 AN: 10914

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31636

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2160

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 511006

Other (OTH) AF: 0.00 AC: 0 AN: 27258

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 980

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		-0.55
PromoterAI		0.14	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs402348;

hg19: chr18-61034420;