1-100172152-G-A

Variant names:

• chr1-100172152-G-A
• rs11166407
• NM_144620.4:c.-79+1179C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000285530 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144620.4. 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
	LRRC39	NM_144620.4	MANE Select	c.-79+1179C>T		intron	N/A	NP_653221.1	Q96DD0-1
	LRRC39	NM_001256385.2		c.-79+1179C>T		intron	N/A	NP_001243314.1	Q96DD0-2
	LRRC39	NM_001256386.2		c.-79+1179C>T		intron	N/A	NP_001243315.1	Q96DD0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC39	ENST00000370137.6	TSL:1 MANE Select	c.-79+1179C>T		intron	N/A	ENSP00000359156.1	Q96DD0-1
	LRRC39	ENST00000370138.1	TSL:5	c.-79+1179C>T		intron	N/A	ENSP00000359157.1	Q96DD0-2
	LRRC39	ENST00000342895.8	TSL:5	c.-79+1179C>T		intron	N/A	ENSP00000344470.3	Q96DD0-1

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

African (AFR) AF: 0.489 AC: 20265 AN: 41418

American (AMR) AF: 0.140 AC: 2135 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3464

East Asian (EAS) AF: 0.0484 AC: 251 AN: 5182

South Asian (SAS) AF: 0.101 AC: 489 AN: 4828

European-Finnish (FIN) AF: 0.0992 AC: 1050 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10131 AN: 67976

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.205 Hom.: 920

Bravo AF: 0.245

Asia WGS AF: 0.124 AC: 431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.15
PhyloP100		-0.93
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: rs11166407; hg19: chr1-100637708;