10-70352092-C-T

Variant names:

• chr10-70352092-C-T
• rs10509322
• NM_001278212.2:c.83-11390G>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.83-11390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,996 control chromosomes in the GnomAD database, including 42,858 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 0.75 (42858 hom., cov: 31)
• Consequence: LRRC20 NM_001278212.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC20	NM_001278212.2	c.83-11390G>A		intron_variant	Intron 2 of 4	ENST00000446961.4	NP_001265141.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC20	ENST00000446961.4	c.83-11390G>A		intron_variant	Intron 2 of 4	2	NM_001278212.2	ENSP00000413745.2

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113552 AN: 151878 Hom.: 42809 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.748 AC: 113648 AN: 151996 Hom.: 42858 Cov.: 31 AF XY: 0.749 AC XY: 55688 AN XY: 74306

African (AFR) AF: 0.678 AC: 28082 AN: 41422

American (AMR) AF: 0.801 AC: 12227 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2683 AN: 3470

East Asian (EAS) AF: 0.660 AC: 3412 AN: 5168

South Asian (SAS) AF: 0.567 AC: 2735 AN: 4820

European-Finnish (FIN) AF: 0.805 AC: 8478 AN: 10538

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53383 AN: 67990

Other (OTH) AF: 0.786 AC: 1658 AN: 2110

Alfa AF: 0.770 Hom.: 165861

Bravo AF: 0.746

Asia WGS AF: 0.598 AC: 2079 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.30
PhyloP100		0.32
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: rs10509322; hg19: chr10-72111848; COSMIC: COSV62939542;