rs10762360

Variant names:

• chr10-70299750-G-C
• rs10762360
• NM_001278212.2:c.*1604C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-70299750-G-C
• chr10-70299750-G-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.*1604C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,842 control chromosomes in the GnomAD database, including 37,733 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 0.70 (37505 hom., cov: 31)
  • Exomes 𝑓: 0.74 (228 hom.)
• Consequence: LRRC20 NM_001278212.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC20	NM_001278212.2	c.*1604C>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000446961.4	NP_001265141.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC20	ENST00000446961.4	c.*1604C>G		3_prime_UTR_variant	Exon 5 of 5	2	NM_001278212.2	ENSP00000413745.2

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106146 AN: 151924 Hom.: 37483 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.674

GnomAD4 exome AF: 0.745 AC: 596 AN: 800 Hom.: 228 Cov.: 0 AF XY: 0.741 AC XY: 461 AN XY: 622

African (AFR) AF: 0.722 AC: 13 AN: 18

American (AMR) AF: 0.417 AC: 5 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 0.412 AC: 14 AN: 34

South Asian (SAS) AF: 0.600 AC: 6 AN: 10

European-Finnish (FIN) AF: 1.00 AC: 16 AN: 16

Middle Eastern (MID) AF: 1.00 AC: 4 AN: 4

European-Non Finnish (NFE) AF: 0.760 AC: 508 AN: 668

Other (OTH) AF: 0.794 AC: 27 AN: 34

GnomAD4 genome AF: 0.699 AC: 106215 AN: 152042 Hom.: 37505 Cov.: 31 AF XY: 0.699 AC XY: 51954 AN XY: 74332

African (AFR) AF: 0.659 AC: 27337 AN: 41476

American (AMR) AF: 0.633 AC: 9675 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2082 AN: 3470

East Asian (EAS) AF: 0.476 AC: 2445 AN: 5138

South Asian (SAS) AF: 0.653 AC: 3152 AN: 4824

European-Finnish (FIN) AF: 0.790 AC: 8358 AN: 10578

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50867 AN: 67972

Other (OTH) AF: 0.670 AC: 1412 AN: 2108

Alfa AF: 0.726 Hom.: 5049

Bravo AF: 0.681

Asia WGS AF: 0.535 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.73
PhyloP100		0.42
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: rs10762360; hg19: chr10-72059506;