chr13-20414206-TACACAC-T

Variant names:

• chr13-20414206-TACACAC-T
• rs55719240
• NM_015974.3:c.634-825_634-820delGTGTGT

Variant summary

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

The NM_015974.3(CRYL1):​c.634-825_634-820delGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.061 (752 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-TACACAC-T is Benign according to our data. Variant chr13-20414206-TACACAC-T is described in ClinVar as Benign. ClinVar VariationId is 1181096.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 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.634-825_634-820delGTGTGT		intron	N/A	NP_057058.2	Q9Y2S2-1
	CRYL1	NM_001363647.2		c.472-825_472-820delGTGTGT		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.634-825_634-820delGTGTGT		intron	N/A	ENSP00000298248.7	Q9Y2S2-1
	CRYL1	ENST00000382812.5	TSL:1	c.568-825_568-820delGTGTGT		intron	N/A	ENSP00000372262.1	Q9Y2S2-2
	CRYL1	ENST00000887623.1		c.595-825_595-820delGTGTGT		intron	N/A	ENSP00000557682.1

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9081 AN: 150368 Hom.: 748 Cov.: 0

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.00174

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.00633

Gnomad FIN AF: 0.00216

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00163

Gnomad OTH AF: 0.0409

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

GnomAD4 genome AF: 0.0605 AC: 9111 AN: 150486 Hom.: 752 Cov.: 0 AF XY: 0.0613 AC XY: 4501 AN XY: 73432

African (AFR) AF: 0.169 AC: 6948 AN: 40998

American (AMR) AF: 0.112 AC: 1695 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.00174 AC: 6 AN: 3456

East Asian (EAS) AF: 0.0420 AC: 213 AN: 5076

South Asian (SAS) AF: 0.00613 AC: 29 AN: 4734

European-Finnish (FIN) AF: 0.00216 AC: 22 AN: 10202

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.00163 AC: 110 AN: 67622

Other (OTH) AF: 0.0410 AC: 85 AN: 2074

Alfa AF: 0.000891 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

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

Other links and lift over

dbSNP: rs55719240; hg19: chr13-20988345;