rs10507539

Variant names:

• chr13-46260571-G-A
• rs10507539
• NM_001282460.2:c.1227-1338G>A

Variant summary

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

The NM_001282460.2(LRRC63):​c.1227-1338G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,994 control chromosomes in the GnomAD database, including 6,895 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 0.29 (6895 hom., cov: 32)
• Consequence: LRRC63 NM_001282460.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351

Genes affected

LRRC63 (HGNC:34296): (leucine rich repeat containing 63) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC63	NM_001282460.2	c.1227-1338G>A		intron_variant	Intron 7 of 9	ENST00000595396.3	NP_001269389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC63	ENST00000595396.3	c.1227-1338G>A		intron_variant	Intron 7 of 9	5	NM_001282460.2	ENSP00000469337.1
LRRC63	ENST00000378805.7	n.1227-1338G>A		intron_variant	Intron 7 of 8	1		ENSP00000368082.3

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44521 AN: 151876 Hom.: 6888 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.293 AC: 44540 AN: 151994 Hom.: 6895 Cov.: 32 AF XY: 0.294 AC XY: 21846 AN XY: 74284

African (AFR) AF: 0.198 AC: 8215 AN: 41486

American (AMR) AF: 0.293 AC: 4472 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3466

East Asian (EAS) AF: 0.392 AC: 2020 AN: 5158

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4816

European-Finnish (FIN) AF: 0.347 AC: 3664 AN: 10558

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22392 AN: 67936

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.321 Hom.: 5834

Bravo AF: 0.287

Asia WGS AF: 0.318 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.71
PhyloP100		0.35
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

Publications

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Other links and lift over

dbSNP: rs10507539; hg19: chr13-46834706;