7-150336793-A-G

Variant names:

• chr7-150336793-A-G
• rs3735171
• NM_001142928.2:c.-69A>G

Variant summary

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

The NM_001142928.2(LRRC61):​c.-69A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,536,328 control chromosomes in the GnomAD database, including 52,867 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 0.27 (5790 hom., cov: 34)
  • Exomes 𝑓: 0.26 (47077 hom.)
• Consequence: LRRC61 NM_001142928.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 18 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142928.2. 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
	LRRC61	NM_001142928.2	MANE Select	c.-69A>G		5_prime_UTR	Exon 3 of 3	NP_001136400.1
	LRRC61	NM_001363433.1		c.-69A>G		5_prime_UTR	Exon 3 of 3	NP_001350362.1
	LRRC61	NM_001363434.1		c.-69A>G		5_prime_UTR	Exon 3 of 3	NP_001350363.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC61	ENST00000359623.9	TSL:2 MANE Select	c.-69A>G		5_prime_UTR	Exon 3 of 3	ENSP00000352642.4
	LRRC61	ENST00000323078.7	TSL:1	c.-69A>G		5_prime_UTR	Exon 2 of 2	ENSP00000339047.6
	LRRC61	ENST00000493307.1	TSL:5	c.-69A>G		5_prime_UTR	Exon 4 of 4	ENSP00000420560.1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41163 AN: 152144 Hom.: 5782 Cov.: 34

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.246

GnomAD4 exome AF: 0.258 AC: 357307 AN: 1384064 Hom.: 47077 Cov.: 31 AF XY: 0.259 AC XY: 176171 AN XY: 680058

African (AFR) AF: 0.339 AC: 10864 AN: 32080

American (AMR) AF: 0.119 AC: 4545 AN: 38286

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 6973 AN: 21580

East Asian (EAS) AF: 0.346 AC: 13524 AN: 39050

South Asian (SAS) AF: 0.282 AC: 21235 AN: 75356

European-Finnish (FIN) AF: 0.257 AC: 10653 AN: 41382

Middle Eastern (MID) AF: 0.246 AC: 1323 AN: 5370

European-Non Finnish (NFE) AF: 0.255 AC: 273413 AN: 1073708

Other (OTH) AF: 0.258 AC: 14777 AN: 57252

GnomAD4 genome AF: 0.271 AC: 41207 AN: 152264 Hom.: 5790 Cov.: 34 AF XY: 0.270 AC XY: 20081 AN XY: 74450

African (AFR) AF: 0.331 AC: 13757 AN: 41552

American (AMR) AF: 0.167 AC: 2557 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1508 AN: 5182

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4824

European-Finnish (FIN) AF: 0.250 AC: 2650 AN: 10610

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17342 AN: 68004

Other (OTH) AF: 0.243 AC: 514 AN: 2112

Alfa AF: 0.248 Hom.: 1233

Bravo AF: 0.264

Asia WGS AF: 0.290 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.020
DANN	Benign	0.38
PhyloP100		-2.2
Mutation Taster		=300/0	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: rs3735171; hg19: chr7-150033882; COSMIC: COSV56231285; COSMIC: COSV56231285;