13-20414206-T-TAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015974.3(CRYL1):c.634-820_634-819insGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3129 hom., cov: 0)
• Consequence: CRYL1 NM_015974.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 13-20414206-T-TAC is Benign according to our data. Variant chr13-20414206-T-TAC is described in ClinVar as [Benign]. Clinvar id is 1286730.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRYL1	NM_015974.3	c.634-820_634-819insGT		intron_variant		ENST00000298248.12
CRYL1	NM_001363647.2	c.472-820_472-819insGT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRYL1	ENST00000298248.12	c.634-820_634-819insGT		intron_variant		1	NM_015974.3	P1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28672 AN: 150296 Hom.: 3126 Cov.: 0

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.191 AC: 28684 AN: 150414 Hom.: 3129 Cov.: 0 AF XY: 0.193 AC XY: 14182 AN XY: 73406

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.204

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

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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;