NM_018214.5:c.160-21635T>C

Variant names:

• chr6-53820475-T-C
• rs4486000
• NM_018214.5:c.160-21635T>C

Variant summary

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

The NM_018214.5(LRRC1):​c.160-21635T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 148,662 control chromosomes in the GnomAD database, including 5,262 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 0.26 (5262 hom., cov: 23)
• Consequence: LRRC1 NM_018214.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC1	NM_018214.5	c.160-21635T>C		intron_variant	Intron 1 of 13	ENST00000370888.6	NP_060684.4
LRRC1	XM_017010997.2	c.160-21635T>C		intron_variant	Intron 1 of 10		XP_016866486.1
LRRC1	XR_001743505.2	n.412-21635T>C		intron_variant	Intron 1 of 11
LRRC1	XR_007059279.1	n.412-21635T>C		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC1	ENST00000370888.6	c.160-21635T>C		intron_variant	Intron 1 of 13	1	NM_018214.5	ENSP00000359925.1
LRRC1	ENST00000370882.1	c.160-21635T>C		intron_variant	Intron 1 of 4	3		ENSP00000359919.1
LRRC1	ENST00000487251.5	n.160-21635T>C		intron_variant	Intron 2 of 10	2		ENSP00000435217.1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39033 AN: 148544 Hom.: 5243 Cov.: 23

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.263 AC: 39085 AN: 148662 Hom.: 5262 Cov.: 23 AF XY: 0.265 AC XY: 19199 AN XY: 72324

African (AFR) AF: 0.284 AC: 11405 AN: 40104

American (AMR) AF: 0.233 AC: 3435 AN: 14760

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 511 AN: 3450

East Asian (EAS) AF: 0.261 AC: 1324 AN: 5068

South Asian (SAS) AF: 0.255 AC: 1168 AN: 4586

European-Finnish (FIN) AF: 0.360 AC: 3609 AN: 10018

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16840 AN: 67428

Other (OTH) AF: 0.234 AC: 481 AN: 2056

Alfa AF: 0.244 Hom.: 8029

Bravo AF: 0.258

Asia WGS AF: 0.275 AC: 957 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	0.074
DANN	Benign	0.31
PhyloP100		-1.4
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: rs4486000; hg19: chr6-53685273;