13-20414206-TACACAC-T

Variant summary

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

The NM_015974.3(CRYL1):c.634-825_634-820del 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

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-TACACAC-T is Benign according to our data. Variant chr13-20414206-TACACAC-T is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRYL1	NM_015974.3	c.634-825_634-820del		intron_variant		ENST00000298248.12
CRYL1	NM_001363647.2	c.472-825_472-820del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRYL1	ENST00000298248.12	c.634-825_634-820del		intron_variant		1	NM_015974.3	P1

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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.00174

Gnomad4 EAS AF: 0.0420

Gnomad4 SAS AF: 0.00613

Gnomad4 FIN AF: 0.00216

Gnomad4 NFE AF: 0.00163

Gnomad4 OTH AF: 0.0410

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 11, 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;