rs4554381

Positions:

• chr7-150328478-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LRRC61	NM_001142928.2	c.-145+2468G>A		intron_variant		ENST00000359623.9	NP_001136400.1
LRRC61	NM_001363433.1	c.-145+2468G>A		intron_variant			NP_001350362.1
LRRC61	NM_001363434.1	c.-145+2468G>A		intron_variant			NP_001350363.1
LRRC61	NM_023942.3	c.-145+4918G>A		intron_variant			NP_076431.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC61	ENST00000359623.9	c.-145+2468G>A		intron_variant		2	NM_001142928.2	ENSP00000352642	P1
	ENST00000343855.6	n.745-157G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.266

Alfa AF: 0.299 Hom.: 972

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs4554381; hg19: chr7-150025567; COSMIC: COSV59605425; COSMIC: COSV59605425;