13-20414206-TACACACACACAC-TACACACACAC

Variant names:

• chr13-20414206-TAC-T
• rs55719240
• NM_015974.3:c.634-821_634-820delGT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015974.3(CRYL1):​c.634-821_634-820delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.024 (137 hom., cov: 0)
• Consequence: CRYL1 NM_015974.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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: Benign. The variant received -10 ACMG points.

• BP6: Variant 13-20414206-TAC-T is Benign according to our data. Variant chr13-20414206-TAC-T is described in ClinVar as Benign. ClinVar VariationId is 1231237.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0738 is higher than 0.05.

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.634-821_634-820delGT		intron	N/A	NP_057058.2	Q9Y2S2-1
	CRYL1	NM_001363647.2		c.472-821_472-820delGT		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.634-821_634-820delGT		intron	N/A	ENSP00000298248.7	Q9Y2S2-1
	CRYL1	ENST00000382812.5	TSL:1	c.568-821_568-820delGT		intron	N/A	ENSP00000372262.1	Q9Y2S2-2
	CRYL1	ENST00000887623.1		c.595-821_595-820delGT		intron	N/A	ENSP00000557682.1

Frequencies

GnomAD3 genomes AF: 0.0242 AC: 3648 AN: 150446 Hom.: 135 Cov.: 0

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.00405

Gnomad EAS AF: 0.00216

Gnomad SAS AF: 0.00169

Gnomad FIN AF: 0.000293

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00362

Gnomad OTH AF: 0.0175

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

GnomAD4 genome AF: 0.0244 AC: 3670 AN: 150562 Hom.: 137 Cov.: 0 AF XY: 0.0242 AC XY: 1780 AN XY: 73468

African (AFR) AF: 0.0760 AC: 3114 AN: 40978

American (AMR) AF: 0.0158 AC: 239 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.00405 AC: 14 AN: 3458

East Asian (EAS) AF: 0.00217 AC: 11 AN: 5080

South Asian (SAS) AF: 0.00169 AC: 8 AN: 4736

European-Finnish (FIN) AF: 0.000293 AC: 3 AN: 10222

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00362 AC: 245 AN: 67666

Other (OTH) AF: 0.0174 AC: 36 AN: 2074

Alfa AF: 0.00468 Hom.: 134

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism

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: rs55719240; hg19: chr13-20988345;