3-169850328-G-C

Position:

• chr3-169850328-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024727.4(LRRC31):​c.1159+1291C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,896 control chromosomes in the GnomAD database, including 7,841 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 0.31 (7841 hom., cov: 32)
• Consequence: LRRC31 NM_024727.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LRRC31 (HGNC:26261): (leucine rich repeat containing 31)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC31	NM_024727.4	c.1159+1291C>G		intron_variant		ENST00000316428.10	NP_079003.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC31	ENST00000316428.10	c.1159+1291C>G		intron_variant		1	NM_024727.4	ENSP00000325978.5
LRRC31	ENST00000523069.1	c.1159+1291C>G		intron_variant		1		ENSP00000429145.1
LRRC31	ENST00000264676.9	c.991+1291C>G		intron_variant		2		ENSP00000264676.5

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47377 AN: 151778 Hom.: 7827 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.312 AC: 47415 AN: 151896 Hom.: 7841 Cov.: 32 AF XY: 0.317 AC XY: 23520 AN XY: 74232

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.302

Alfa AF: 0.170 Hom.: 317

Bravo AF: 0.319

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
DANN	Benign	0.53

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: rs16847897; hg19: chr3-169568116;