6-53843517-C-T

Variant names:

• chr6-53843517-C-T
• rs7763081
• NM_018214.5:c.277+1290C>T

Variant summary

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

The NM_018214.5(LRRC1):​c.277+1290C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,242 control chromosomes in the GnomAD database, including 52,582 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 0.83 (52582 hom., cov: 34)
• Consequence: LRRC1 NM_018214.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 3 publications found

Genes affected

LRRC1 (HGNC:14307): (leucine rich repeat containing 1) Located in cytosol. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018214.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC1	NM_018214.5	MANE Select	c.277+1290C>T		intron	N/A	NP_060684.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC1	ENST00000370888.6	TSL:1 MANE Select	c.277+1290C>T		intron	N/A	ENSP00000359925.1
	LRRC1	ENST00000370882.1	TSL:3	c.277+1290C>T		intron	N/A	ENSP00000359919.1
	LRRC1	ENST00000487251.5	TSL:2	n.277+1290C>T		intron	N/A	ENSP00000435217.1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126170 AN: 152124 Hom.: 52538 Cov.: 34

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.829 AC: 126269 AN: 152242 Hom.: 52582 Cov.: 34 AF XY: 0.829 AC XY: 61682 AN XY: 74446

African (AFR) AF: 0.764 AC: 31697 AN: 41498

American (AMR) AF: 0.879 AC: 13454 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2768 AN: 3472

East Asian (EAS) AF: 0.964 AC: 5002 AN: 5188

South Asian (SAS) AF: 0.861 AC: 4152 AN: 4824

European-Finnish (FIN) AF: 0.796 AC: 8444 AN: 10608

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57920 AN: 68036

Other (OTH) AF: 0.855 AC: 1805 AN: 2112

Alfa AF: 0.826 Hom.: 6708

Bravo AF: 0.837

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.70
PhyloP100		0.12
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: rs7763081; hg19: chr6-53708315;