10-70354622-T-C

Variant names:

• chr10-70354622-T-C
• rs4747011
• NM_001278212.2:c.83-13920A>G

Variant summary

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

The NM_001278212.2(LRRC20):​c.83-13920A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,180 control chromosomes in the GnomAD database, including 65,861 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 0.93 (65861 hom., cov: 31)
• Consequence: LRRC20 NM_001278212.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.959 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.83-13920A>G		intron	N/A	NP_001265141.1	Q8TCA0-1
	LRRC20	NM_001278211.2		c.83-13920A>G		intron	N/A	NP_001265140.1	Q8TCA0-1
	LRRC20	NM_207119.3		c.83-13920A>G		intron	N/A	NP_997002.1	Q8TCA0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC20	ENST00000446961.4	TSL:2 MANE Select	c.83-13920A>G		intron	N/A	ENSP00000413745.2	Q8TCA0-1
	LRRC20	ENST00000355790.8	TSL:1	c.83-13920A>G		intron	N/A	ENSP00000348043.4	Q8TCA0-1
	LRRC20	ENST00000373224.5	TSL:2	c.83-13920A>G		intron	N/A	ENSP00000362321.1	Q8TCA0-1

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141350 AN: 152062 Hom.: 65819 Cov.: 31

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.954

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

GnomAD4 genome AF: 0.929 AC: 141448 AN: 152180 Hom.: 65861 Cov.: 31 AF XY: 0.929 AC XY: 69086 AN XY: 74390

African (AFR) AF: 0.890 AC: 36913 AN: 41478

American (AMR) AF: 0.972 AC: 14874 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.981 AC: 3407 AN: 3472

East Asian (EAS) AF: 0.908 AC: 4702 AN: 5178

South Asian (SAS) AF: 0.869 AC: 4181 AN: 4814

European-Finnish (FIN) AF: 0.913 AC: 9688 AN: 10606

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64491 AN: 68010

Other (OTH) AF: 0.954 AC: 2016 AN: 2114

Alfa AF: 0.945 Hom.: 205462

Bravo AF: 0.935

Asia WGS AF: 0.884 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.48
PhyloP100		-2.3
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: rs4747011; hg19: chr10-72114378;