10-70354622-T-C

Position:

• chr10-70354622-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC20	NM_001278212.2	c.83-13920A>G		intron_variant		ENST00000446961.4	NP_001265141.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC20	ENST00000446961.4	c.83-13920A>G		intron_variant		2	NM_001278212.2	ENSP00000413745	P1

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

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.981

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.948

Gnomad4 OTH AF: 0.954

Alfa AF: 0.950 Hom.: 91383

Bravo AF: 0.935

Asia WGS AF: 0.884 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs4747011; hg19: chr10-72114378;