13-20414206-TACACACACACAC-TACACACAC

Variant names:

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

Variant summary

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

The NM_015974.3(CRYL1):​c.634-823_634-820delGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.71 (37690 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-TACAC-T is Benign according to our data. Variant chr13-20414206-TACAC-T is described in ClinVar as Benign. ClinVar VariationId is 1271792.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 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.634-823_634-820delGTGT		intron	N/A	NP_057058.2	Q9Y2S2-1
	CRYL1	NM_001363647.2		c.472-823_472-820delGTGT		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.634-823_634-820delGTGT		intron	N/A	ENSP00000298248.7	Q9Y2S2-1
	CRYL1	ENST00000382812.5	TSL:1	c.568-823_568-820delGTGT		intron	N/A	ENSP00000372262.1	Q9Y2S2-2
	CRYL1	ENST00000887623.1		c.595-823_595-820delGTGT		intron	N/A	ENSP00000557682.1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 106230 AN: 150374 Hom.: 37680 Cov.: 0

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.706 AC: 106284 AN: 150492 Hom.: 37690 Cov.: 0 AF XY: 0.704 AC XY: 51710 AN XY: 73450

African (AFR) AF: 0.624 AC: 25584 AN: 40968

American (AMR) AF: 0.716 AC: 10844 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2604 AN: 3456

East Asian (EAS) AF: 0.648 AC: 3288 AN: 5072

South Asian (SAS) AF: 0.754 AC: 3566 AN: 4728

European-Finnish (FIN) AF: 0.712 AC: 7267 AN: 10212

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.750 AC: 50725 AN: 67648

Other (OTH) AF: 0.719 AC: 1489 AN: 2072

Alfa AF: 0.735 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 (auto)

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;