NM_001278212.2:c.401-2834G>T

Variant names:

• chr10-70304342-C-A
• rs10762363
• NM_001278212.2:c.401-2834G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278212.2(LRRC20):​c.401-2834G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,154 control chromosomes in the GnomAD database, including 8,077 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 0.31 (8077 hom., cov: 28)
• Consequence: LRRC20 NM_001278212.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 2 publications found

Genes affected

LRRC20 (HGNC:23421): (leucine rich repeat containing 20)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278212.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC20	NM_001278212.2	MANE Select	c.401-2834G>T		intron	N/A	NP_001265141.1
	LRRC20	NM_001278211.2		c.401-2834G>T		intron	N/A	NP_001265140.1
	LRRC20	NM_207119.3		c.401-2834G>T		intron	N/A	NP_997002.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC20	ENST00000446961.4	TSL:2 MANE Select	c.401-2834G>T		intron	N/A	ENSP00000413745.2
	LRRC20	ENST00000355790.8	TSL:1	c.401-2834G>T		intron	N/A	ENSP00000348043.4
	LRRC20	ENST00000373224.5	TSL:2	c.401-2834G>T		intron	N/A	ENSP00000362321.1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47019 AN: 151036 Hom.: 8073 Cov.: 28

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.311 AC: 47032 AN: 151154 Hom.: 8077 Cov.: 28 AF XY: 0.313 AC XY: 23079 AN XY: 73746

African (AFR) AF: 0.208 AC: 8577 AN: 41282

American (AMR) AF: 0.268 AC: 4068 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3458

East Asian (EAS) AF: 0.0953 AC: 491 AN: 5154

South Asian (SAS) AF: 0.258 AC: 1235 AN: 4788

European-Finnish (FIN) AF: 0.498 AC: 5130 AN: 10300

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25690 AN: 67702

Other (OTH) AF: 0.288 AC: 603 AN: 2096

Alfa AF: 0.351 Hom.: 1219

Bravo AF: 0.286

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		0.28
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: rs10762363; hg19: chr10-72064098;