rs11166407

chr1-100172152-G-Achr1-100172152-G-C

Variant summary

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

The NM_144620.4(LRRC39):c.-79+1179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,046 control chromosomes in the GnomAD database, including 6,146 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 0.23 (6146 hom., cov: 31)
• Consequence: LRRC39 NM_144620.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931

Genes affected

LRRC39 (HGNC:28228): (leucine rich repeat containing 39) Predicted to enable protein serine/threonine phosphatase activity. Predicted to be involved in signal transduction. Predicted to be located in M band. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC39	NM_144620.4	c.-79+1179C>T		intron_variant		ENST00000370137.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC39	ENST00000370137.6	c.-79+1179C>T		intron_variant		1	NM_144620.4	P1
LRRC39	ENST00000342895.8	c.-79+1179C>T		intron_variant		5		P1
LRRC39	ENST00000370138.1	c.-79+1179C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35266 AN: 151926 Hom.: 6120 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.232 AC: 35341 AN: 152046 Hom.: 6146 Cov.: 31 AF XY: 0.226 AC XY: 16775 AN XY: 74324

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.201

Alfa AF: 0.198 Hom.: 832

Bravo AF: 0.245

Asia WGS AF: 0.124 AC: 431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.74
Dann	Benign	0.15

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: rs11166407; hg19: chr1-100637708;