rs11595603

Variant names:

• chr10-70380313-C-T
• rs11595603
• NM_001278212.2:c.-64+2236G>A

Variant summary

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

The NM_001278212.2(LRRC20):​c.-64+2236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 152,218 control chromosomes in the GnomAD database, including 256 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 0.050 (256 hom., cov: 32)
• Consequence: LRRC20 NM_001278212.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870
• Publications: 0 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC20	NM_001278212.2	MANE Select	c.-64+2236G>A		intron	N/A	NP_001265141.1
	LRRC20	NM_001278211.2		c.-64+2181G>A		intron	N/A	NP_001265140.1
	LRRC20	NM_207119.3		c.-64+1187G>A		intron	N/A	NP_997002.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC20	ENST00000446961.4	TSL:2 MANE Select	c.-64+2236G>A		intron	N/A	ENSP00000413745.2
	LRRC20	ENST00000355790.8	TSL:1	c.-64+1187G>A		intron	N/A	ENSP00000348043.4
	LRRC20	ENST00000373224.5	TSL:2	c.-64+2181G>A		intron	N/A	ENSP00000362321.1

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7592 AN: 152100 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0499 AC: 7598 AN: 152218 Hom.: 256 Cov.: 32 AF XY: 0.0500 AC XY: 3719 AN XY: 74434

African (AFR) AF: 0.0700 AC: 2906 AN: 41524

American (AMR) AF: 0.0409 AC: 625 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3468

East Asian (EAS) AF: 0.0237 AC: 123 AN: 5188

South Asian (SAS) AF: 0.147 AC: 709 AN: 4816

European-Finnish (FIN) AF: 0.0121 AC: 128 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0390 AC: 2655 AN: 67992

Other (OTH) AF: 0.0578 AC: 122 AN: 2110

Alfa AF: 0.0444 Hom.: 323

Bravo AF: 0.0505

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.58
PhyloP100		0.87
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: rs11595603; hg19: chr10-72140069;