13-20414206-TACAC-T

Position:

• chr13-20414206-TACAC-T

Variant summary

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

The NM_015974.3(CRYL1):​c.634-823_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

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]

CRYL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRYL1	NM_015974.3	c.634-823_634-820delGTGT		intron_variant		ENST00000298248.12	NP_057058.2
CRYL1	NM_001363647.2	c.472-823_472-820delGTGT		intron_variant			NP_001350576.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRYL1	ENST00000298248.12	c.634-823_634-820delGTGT		intron_variant		1	NM_015974.3	ENSP00000298248.7

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

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.719

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: rs55719240; hg19: chr13-20988345;