rs1920773

Positions:

• chr12-91052319-T-A
• chr12-91052319-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007035.4(KERA):​c.887-801A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 151,316 control chromosomes in the GnomAD database, including 57,882 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 0.87 (57882 hom., cov: 30)
• Consequence: KERA NM_007035.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

Genes affected

KERA (HGNC:6309): (keratocan) The protein encoded by this gene is a keratan sulfate proteoglycan that is involved in corneal transparency. Defects in this gene are a cause of autosomal recessive cornea plana 2 (CNA2).[provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KERA	NM_007035.4	c.887-801A>T		intron_variant		ENST00000266719.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KERA	ENST00000266719.4	c.887-801A>T		intron_variant		1	NM_007035.4	P1

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132162 AN: 151198 Hom.: 57840 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.874 AC: 132255 AN: 151316 Hom.: 57882 Cov.: 30 AF XY: 0.878 AC XY: 64919 AN XY: 73942

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.871

Alfa AF: 0.879 Hom.: 7302

Bravo AF: 0.869

Asia WGS AF: 0.938 AC: 3257 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.63

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: rs1920773; hg19: chr12-91446096;