13-20414206-TACACACACACAC-TACACACACACACACAC

Variant names:

• chr13-20414206-T-TACAC
• rs55719240
• NM_015974.3:c.634-823_634-820dupGTGT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015974.3(CRYL1):​c.634-823_634-820dupGTGT 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 0.0017 (1 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: CRYL1 NM_015974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015974.3. 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
	CRYL1	NM_015974.3	MANE Select	c.634-823_634-820dupGTGT		intron	N/A	NP_057058.2	Q9Y2S2-1
	CRYL1	NM_001363647.2		c.472-823_472-820dupGTGT		intron	N/A	NP_001350576.1	A0A2R8Y4K2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYL1	ENST00000298248.12	TSL:1 MANE Select	c.634-820_634-819insGTGT		intron	N/A	ENSP00000298248.7	Q9Y2S2-1
	CRYL1	ENST00000382812.5	TSL:1	c.568-820_568-819insGTGT		intron	N/A	ENSP00000372262.1	Q9Y2S2-2
	CRYL1	ENST00000887623.1		c.595-820_595-819insGTGT		intron	N/A	ENSP00000557682.1

Frequencies

GnomAD3 genomes AF: 0.00175 AC: 264 AN: 150494 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00127

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00112

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00157

Gnomad SAS AF: 0.00633

Gnomad FIN AF: 0.00117

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00204

Gnomad OTH AF: 0.000975

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00175 AC: 263 AN: 150612 Hom.: 1 Cov.: 0 AF XY: 0.00166 AC XY: 122 AN XY: 73502

African (AFR) AF: 0.00127 AC: 52 AN: 41020

American (AMR) AF: 0.00112 AC: 17 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3458

East Asian (EAS) AF: 0.00157 AC: 8 AN: 5080

South Asian (SAS) AF: 0.00633 AC: 30 AN: 4736

European-Finnish (FIN) AF: 0.00117 AC: 12 AN: 10224

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.00204 AC: 138 AN: 67672

Other (OTH) AF: 0.000964 AC: 2 AN: 2074

Alfa AF: 0.000223 Hom.: 134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.52

Splicing

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: rs55719240; hg19: chr13-20988345;