rs1983440

Variant names:

• chr7-150326852-G-C
• rs1983440
• NM_001142928.2:c.-145+842G>C

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+842G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,076 control chromosomes in the GnomAD database, including 5,160 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 (5160 hom., cov: 32)
• Consequence: LRRC61 NM_001142928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 8 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=-0.93).
• 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+842G>C		intron_variant	Intron 2 of 2	ENST00000359623.9	NP_001136400.1
LRRC61	NM_001363433.1	c.-145+842G>C		intron_variant	Intron 2 of 2		NP_001350362.1
LRRC61	NM_001363434.1	c.-145+842G>C		intron_variant	Intron 2 of 2		NP_001350363.1
LRRC61	NM_023942.3	c.-145+3292G>C		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+842G>C		intron_variant	Intron 2 of 2	2	NM_001142928.2	ENSP00000352642.4

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38861 AN: 151956 Hom.: 5167 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.256 AC: 38871 AN: 152076 Hom.: 5160 Cov.: 32 AF XY: 0.259 AC XY: 19269 AN XY: 74326

African (AFR) AF: 0.239 AC: 9898 AN: 41468

American (AMR) AF: 0.185 AC: 2835 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1104 AN: 3472

East Asian (EAS) AF: 0.419 AC: 2166 AN: 5166

South Asian (SAS) AF: 0.291 AC: 1405 AN: 4828

European-Finnish (FIN) AF: 0.307 AC: 3245 AN: 10566

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17290 AN: 67966

Other (OTH) AF: 0.237 AC: 500 AN: 2108

Alfa AF: 0.263 Hom.: 564

Bravo AF: 0.246

Asia WGS AF: 0.339 AC: 1181 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	0.020
DANN	Benign	0.63
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1983440; hg19: chr7-150023941;