8-144522244-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014665.4(LRRC14):​c.*766T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000537 in 372,518 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
Exomes 𝑓: 0.0000054 ( 0 hom. )

Consequence

LRRC14
NM_014665.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.17
Variant links:
Genes affected
LRRC14 (HGNC:20419): (leucine rich repeat containing 14) This gene encodes a leucine-rich repeat-containing protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
LRRC24 (HGNC:28947): (leucine rich repeat containing 24) Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LRRC14NM_014665.4 linkc.*766T>G 3_prime_UTR_variant Exon 4 of 4 ENST00000292524.6 NP_055480.1 Q15048
LRRC24NM_001024678.4 linkc.*231A>C downstream_gene_variant ENST00000529415.7 NP_001019849.2 Q50LG9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LRRC14ENST00000292524.6 linkc.*766T>G 3_prime_UTR_variant Exon 4 of 4 1 NM_014665.4 ENSP00000292524.1 Q15048
LRRC24ENST00000529415.7 linkc.*231A>C downstream_gene_variant 1 NM_001024678.4 ENSP00000434849.1 Q50LG9
LRRC14ENST00000529022.5 linkc.*766T>G downstream_gene_variant 1 ENSP00000434768.1 Q15048
LRRC24ENST00000533758.1 linkc.*231A>C downstream_gene_variant 5 ENSP00000435653.1 G3V1D8

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
0.00000537
AC:
2
AN:
372518
Hom.:
0
Cov.:
6
AF XY:
0.00000530
AC XY:
1
AN XY:
188636
show subpopulations
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:
0.00000759
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.9
DANN
Benign
0.53

Splicing

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: chr8-145747628; API