rs3735171

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-150336793-A-G
• chr7-150336793-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC61	NM_001142928.2	c.-69A>G		5_prime_UTR_variant	Exon 3 of 3	ENST00000359623.9	NP_001136400.1
LRRC61	NM_001363433.1	c.-69A>G		5_prime_UTR_variant	Exon 3 of 3		NP_001350362.1
LRRC61	NM_001363434.1	c.-69A>G		5_prime_UTR_variant	Exon 3 of 3		NP_001350363.1
LRRC61	NM_023942.3	c.-69A>G		5_prime_UTR_variant	Exon 2 of 2		NP_076431.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC61	ENST00000359623	c.-69A>G		5_prime_UTR_variant	Exon 3 of 3	2	NM_001142928.2	ENSP00000352642.4
LRRC61	ENST00000323078	c.-69A>G		5_prime_UTR_variant	Exon 2 of 2	1		ENSP00000339047.6
LRRC61	ENST00000493307	c.-69A>G		5_prime_UTR_variant	Exon 4 of 4	5		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

Gnomad4 AFR exome AF: 0.339

Gnomad4 AMR exome AF: 0.119

Gnomad4 ASJ exome AF: 0.323

Gnomad4 EAS exome AF: 0.346

Gnomad4 SAS exome AF: 0.282

Gnomad4 FIN exome AF: 0.257

Gnomad4 NFE exome AF: 0.255

Gnomad4 OTH exome AF: 0.258

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

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.243

Alfa AF: 0.254 Hom.: 1121

Bravo AF: 0.264

Asia WGS AF: 0.290 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.020
DANN	Benign	0.38

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: rs3735171; hg19: chr7-150033882; COSMIC: COSV56231285; COSMIC: COSV56231285;