rs766522161

Variant names:

• chr3-157028262-C-G
• NM_001004316.3:c.1528C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-157028262-C-G
• chr3-157028262-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001004316.3(LEKR1):​c.1528C>G​(p.Arg510Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000089 in 1,461,284 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000089 (0 hom.)
• Consequence: LEKR1 NM_001004316.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.82

Genes affected

LEKR1 (HGNC:33765): (leucine, glutamate and lysine rich 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LEKR1	NM_001004316.3	c.1528C>G	p.Arg510Gly	missense_variant	Exon 12 of 13	ENST00000356539.9	NP_001004316.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LEKR1	ENST00000356539.9	c.1528C>G	p.Arg510Gly	missense_variant	Exon 12 of 13	5	NM_001004316.3	ENSP00000348936.4
LEKR1	ENST00000470811.6	n.*1006C>G		non_coding_transcript_exon_variant	Exon 13 of 14	2		ENSP00000418214.2
LEKR1	ENST00000470811.6	n.*1006C>G		3_prime_UTR_variant	Exon 13 of 14	2		ENSP00000418214.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000890 AC: 13 AN: 1461284 Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6 AN XY: 726930

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000117

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.038	T
BayesDel_noAF	Benign	-0.29
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.11	T;.
Eigen	Uncertain	0.66
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.77	T;T
M_CAP	Benign	0.028	D
MetaRNN	Uncertain	0.44	T;T
MetaSVM	Benign	-0.70	T
MutationAssessor	Uncertain	2.2	M;.
PrimateAI	Benign	0.28	T
PROVEAN	Uncertain	-4.3	D;D
REVEL	Benign	0.14
Sift	Uncertain	0.0080	D;D
Sift4G	Benign	0.31	T;T
Polyphen		1.0	D;.
Vest4		0.50
MutPred		0.13		Loss of MoRF binding (P = 0.0738);.;
MVP		0.49
ClinPred		0.99	D
GERP RS		5.5
Varity_R		0.27

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-156746051;