13-20414254-T-TG

Variant summary

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

The NM_015974.3(CRYL1):c.634-868_634-867insC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 149,568 control chromosomes in the GnomAD database, including 231 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.034 (231 hom., cov: 30)
• Consequence: CRYL1 NM_015974.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.32

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 13-20414254-T-TG is Benign according to our data. Variant chr13-20414254-T-TG is described in ClinVar as [Benign]. Clinvar id is 1276026.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRYL1	NM_015974.3	c.634-868_634-867insC		intron_variant		ENST00000298248.12
CRYL1	NM_001363647.2	c.472-868_472-867insC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRYL1	ENST00000298248.12	c.634-868_634-867insC		intron_variant		1	NM_015974.3	P1

Frequencies

GnomAD3 genomes AF: 0.0339 AC: 5060 AN: 149462 Hom.: 231 Cov.: 30

Gnomad AFR AF: 0.0806

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0317

Gnomad SAS AF: 0.00478

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.000868

Gnomad OTH AF: 0.0309

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

GnomAD4 genome AF: 0.0339 AC: 5076 AN: 149568 Hom.: 231 Cov.: 30 AF XY: 0.0351 AC XY: 2569 AN XY: 73104

Gnomad4 AFR AF: 0.0807

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.00458

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.000868

Gnomad4 OTH AF: 0.0311

Alfa AF: 0.000447 Hom.: 0

Asia WGS AF: 0.0310 AC: 106 AN: 3476

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

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs879313627; hg19: chr13-20988393;