rs7989332

Variant names:

• chr13-20476436-A-C
• rs7989332
• NM_015974.3:c.276+12934T>G

Your query was ambiguous. Multiple possible variants found:

• chr13-20476436-A-C
• chr13-20476436-A-G
• chr13-20476436-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015974.3(CRYL1):​c.276+12934T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 151,866 control chromosomes in the GnomAD database, including 43,306 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.75 (43306 hom., cov: 30)
• Consequence: CRYL1 NM_015974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 24 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 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.276+12934T>G		intron	N/A	NP_057058.2	Q9Y2S2-1
	CRYL1	NM_001363647.2		c.276+12934T>G		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.276+12934T>G		intron	N/A	ENSP00000298248.7	Q9Y2S2-1
	CRYL1	ENST00000382812.5	TSL:1	c.210+12934T>G		intron	N/A	ENSP00000372262.1	Q9Y2S2-2
	CRYL1	ENST00000887623.1		c.237+12934T>G		intron	N/A	ENSP00000557682.1

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114262 AN: 151752 Hom.: 43263 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.753 AC: 114357 AN: 151866 Hom.: 43306 Cov.: 30 AF XY: 0.753 AC XY: 55874 AN XY: 74218

African (AFR) AF: 0.815 AC: 33705 AN: 41374

American (AMR) AF: 0.797 AC: 12163 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2595 AN: 3470

East Asian (EAS) AF: 0.798 AC: 4117 AN: 5158

South Asian (SAS) AF: 0.774 AC: 3730 AN: 4818

European-Finnish (FIN) AF: 0.670 AC: 7046 AN: 10520

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48619 AN: 67944

Other (OTH) AF: 0.761 AC: 1605 AN: 2108

Alfa AF: 0.738 Hom.: 72627

Bravo AF: 0.765

Asia WGS AF: 0.786 AC: 2731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.40
PhyloP100		-0.097
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7989332; hg19: chr13-21050575;