chr8-91161887-G-A

Variant names:

• chr8-91161887-G-A
• rs4609161
• NM_001129890.2:c.651+26148G>A

Variant summary

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

The NM_001129890.2(LRRC69):​c.651+26148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,134 control chromosomes in the GnomAD database, including 5,441 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 0.21 (5441 hom., cov: 32)
• Consequence: LRRC69 NM_001129890.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 publications found

Genes affected

LRRC69 (HGNC:34303): (leucine rich repeat containing 69) Predicted to be involved in signal transduction. [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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001129890.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC69	NM_001129890.2	MANE Select	c.651+26148G>A		intron	N/A	NP_001123362.1
	LRRC69	NM_001354470.2		c.184-27635G>A		intron	N/A	NP_001341399.1
	LRRC69	NR_148895.2		n.1093+26148G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC69	ENST00000448384.3	TSL:5 MANE Select	c.651+26148G>A		intron	N/A	ENSP00000400803.2
	LRRC69	ENST00000343709.7	TSL:2	c.184-27635G>A		intron	N/A	ENSP00000343221.3
	LRRC69	ENST00000520099.5	TSL:2	n.*840+26148G>A		intron	N/A	ENSP00000428537.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31752 AN: 151016 Hom.: 5424 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.210 AC: 31810 AN: 151134 Hom.: 5441 Cov.: 32 AF XY: 0.202 AC XY: 14934 AN XY: 73798

African (AFR) AF: 0.467 AC: 19308 AN: 41306

American (AMR) AF: 0.136 AC: 2054 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3458

East Asian (EAS) AF: 0.0305 AC: 156 AN: 5122

South Asian (SAS) AF: 0.0591 AC: 285 AN: 4824

European-Finnish (FIN) AF: 0.0713 AC: 741 AN: 10394

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8133 AN: 67636

Other (OTH) AF: 0.184 AC: 385 AN: 2098

Alfa AF: 0.143 Hom.: 964

Bravo AF: 0.226

Asia WGS AF: 0.0790 AC: 276 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.20
PhyloP100		-1.1
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: rs4609161; hg19: chr8-92174115;