chr6-53822917-C-T

Variant names:

• chr6-53822917-C-T
• rs9474661
• NM_018214.5:c.160-19193C>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.160-19193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,028 control chromosomes in the GnomAD database, including 5,473 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 0.27 (5473 hom., cov: 32)
• Consequence: LRRC1 NM_018214.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC1	NM_018214.5	c.160-19193C>T		intron_variant	Intron 1 of 13	ENST00000370888.6	NP_060684.4
LRRC1	XM_017010997.2	c.160-19193C>T		intron_variant	Intron 1 of 10		XP_016866486.1
LRRC1	XR_001743505.2	n.412-19193C>T		intron_variant	Intron 1 of 11
LRRC1	XR_007059279.1	n.412-19193C>T		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC1	ENST00000370888.6	c.160-19193C>T		intron_variant	Intron 1 of 13	1	NM_018214.5	ENSP00000359925.1
LRRC1	ENST00000370882.1	c.160-19193C>T		intron_variant	Intron 1 of 4	3		ENSP00000359919.1
LRRC1	ENST00000487251.5	n.160-19193C>T		intron_variant	Intron 2 of 10	2		ENSP00000435217.1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40241 AN: 151910 Hom.: 5449 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.265 AC: 40300 AN: 152028 Hom.: 5473 Cov.: 32 AF XY: 0.268 AC XY: 19943 AN XY: 74296

African (AFR) AF: 0.289 AC: 11987 AN: 41468

American (AMR) AF: 0.236 AC: 3601 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5180

South Asian (SAS) AF: 0.256 AC: 1232 AN: 4806

European-Finnish (FIN) AF: 0.362 AC: 3817 AN: 10548

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16998 AN: 67968

Other (OTH) AF: 0.237 AC: 500 AN: 2110

Alfa AF: 0.253 Hom.: 2143

Bravo AF: 0.258

Asia WGS AF: 0.276 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.64
PhyloP100		-0.75
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: rs9474661; hg19: chr6-53687715;