rs4554381

Variant names:

• chr7-150328478-G-A
• rs4554381
• NM_001142928.2:c.-145+2468G>A

Variant summary

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

The NM_001142928.2(LRRC61):​c.-145+2468G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,122 control chromosomes in the GnomAD database, including 7,008 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 0.30 (7008 hom., cov: 33)
• Consequence: LRRC61 NM_001142928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 7 publications found

Genes affected

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000293476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC61	NM_001142928.2	c.-145+2468G>A		intron_variant	Intron 2 of 2	ENST00000359623.9	NP_001136400.1
LRRC61	NM_001363433.1	c.-145+2468G>A		intron_variant	Intron 2 of 2		NP_001350362.1
LRRC61	NM_001363434.1	c.-145+2468G>A		intron_variant	Intron 2 of 2		NP_001350363.1
LRRC61	NM_023942.3	c.-145+4918G>A		intron_variant	Intron 1 of 1		NP_076431.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC61	ENST00000359623.9	c.-145+2468G>A		intron_variant	Intron 2 of 2	2	NM_001142928.2	ENSP00000352642.4

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44985 AN: 152002 Hom.: 7000 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.296 AC: 45024 AN: 152122 Hom.: 7008 Cov.: 33 AF XY: 0.298 AC XY: 22153 AN XY: 74360

African (AFR) AF: 0.379 AC: 15737 AN: 41490

American (AMR) AF: 0.198 AC: 3029 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1105 AN: 3466

East Asian (EAS) AF: 0.420 AC: 2174 AN: 5176

South Asian (SAS) AF: 0.292 AC: 1410 AN: 4826

European-Finnish (FIN) AF: 0.309 AC: 3272 AN: 10580

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17304 AN: 67972

Other (OTH) AF: 0.266 AC: 562 AN: 2112

Alfa AF: 0.302 Hom.: 1024

Bravo AF: 0.292

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.85
PhyloP100		0.035
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: rs4554381; hg19: chr7-150025567; COSMIC: COSV59605425; COSMIC: COSV59605425;