rs55719240

Variant names:

• chr13-20414206-TACACACACACAC-T
• rs55719240
• NM_015974.3:c.634-831_634-820delGTGTGTGTGTGT

Your query was ambiguous. Multiple possible variants found:

• chr13-20414206-TACACACACACAC-T
• chr13-20414206-TACACACACACAC-TAC
• chr13-20414206-TACACACACACAC-TACAC
• chr13-20414206-TACACACACACAC-TACACAC
• chr13-20414206-TACACACACACAC-TACACACAC
• chr13-20414206-TACACACACACAC-TACACACACAC
• chr13-20414206-TACACACACACAC-TACACACACACACAC
• chr13-20414206-TACACACACACAC-TACACACACACACACAC
• chr13-20414206-TACACACACACAC-TACACACACACACACACAC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_015974.3(CRYL1):​c.634-831_634-820delGTGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 0)
• Consequence: CRYL1 NM_015974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

CRYL1 (HGNC:18246): (crystallin lambda 1) The uronate cycle functions as an alternative glucose metabolic pathway, accounting for about 5% of daily glucose catabolism. The product of this gene catalyzes the dehydrogenation of L-gulonate into dehydro-L-gulonate in the uronate cycle. The enzyme requires NAD(H) as a coenzyme, and is inhibited by inorganic phosphate. A similar gene in the rabbit is thought to serve a structural role in the lens of the eye. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRYL1	NM_015974.3	c.634-831_634-820delGTGTGTGTGTGT		intron_variant	Intron 5 of 7	ENST00000298248.12	NP_057058.2
CRYL1	NM_001363647.2	c.472-831_472-820delGTGTGTGTGTGT		intron_variant	Intron 4 of 6		NP_001350576.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRYL1	ENST00000298248.12	c.634-831_634-820delGTGTGTGTGTGT		intron_variant	Intron 5 of 7	1	NM_015974.3	ENSP00000298248.7

Frequencies

GnomAD3 genomes AF: 0.00000664 AC: 1 AN: 150494 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000245

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000664 AC: 1 AN: 150494 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 73374

Gnomad4 AFR AF: 0.0000245

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55719240; hg19: chr13-20988345;