6-53880679-C-T

Position:

• chr6-53880679-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018214.5(LRRC1):​c.356+1608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 152,208 control chromosomes in the GnomAD database, including 900 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 0.087 (900 hom., cov: 32)
• Consequence: LRRC1 NM_018214.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

LRRC1 (HGNC:14307): (leucine rich repeat containing 1) Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC1	NM_018214.5	c.356+1608C>T		intron_variant		ENST00000370888.6	NP_060684.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC1	ENST00000370888.6	c.356+1608C>T		intron_variant		1	NM_018214.5	ENSP00000359925.1
LRRC1	ENST00000370882.1	c.356+1608C>T		intron_variant		3		ENSP00000359919.1
LRRC1	ENST00000487251.5	n.356+1608C>T		intron_variant		2		ENSP00000435217.1

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13205 AN: 152090 Hom.: 893 Cov.: 32

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0869 AC: 13230 AN: 152208 Hom.: 900 Cov.: 32 AF XY: 0.0909 AC XY: 6762 AN XY: 74414

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.0771

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0873

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0839 Hom.: 89

Bravo AF: 0.0936

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.76

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: rs9395885; hg19: chr6-53745477;