3-169841446-G-A

Variant names:

• chr3-169841446-G-A
• rs16854453
• NM_024727.4:c.1328-1133C>T

Variant summary

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

The NM_024727.4(LRRC31):​c.1328-1133C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,064 control chromosomes in the GnomAD database, including 5,515 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 0.25 (5515 hom., cov: 32)
• Consequence: LRRC31 NM_024727.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 12 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024727.4. 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
	LRRC31	NM_024727.4	MANE Select	c.1328-1133C>T		intron	N/A	NP_079003.2
	LRRC31	NM_001277128.2		c.1160-1133C>T		intron	N/A	NP_001264057.1
	LRRC31	NM_001277127.2		c.1328-1115C>T		intron	N/A	NP_001264056.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC31	ENST00000316428.10	TSL:1 MANE Select	c.1328-1133C>T		intron	N/A	ENSP00000325978.5
	LRRC31	ENST00000523069.1	TSL:1	c.1328-1115C>T		intron	N/A	ENSP00000429145.1
	LRRC31	ENST00000264676.9	TSL:2	c.1160-1133C>T		intron	N/A	ENSP00000264676.5

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38280 AN: 151946 Hom.: 5505 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.252 AC: 38298 AN: 152064 Hom.: 5515 Cov.: 32 AF XY: 0.255 AC XY: 18953 AN XY: 74336

African (AFR) AF: 0.163 AC: 6762 AN: 41476

American (AMR) AF: 0.337 AC: 5141 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3217 AN: 5180

South Asian (SAS) AF: 0.259 AC: 1250 AN: 4824

European-Finnish (FIN) AF: 0.286 AC: 3017 AN: 10550

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17346 AN: 67988

Other (OTH) AF: 0.251 AC: 528 AN: 2104

Alfa AF: 0.262 Hom.: 6107

Bravo AF: 0.256

Asia WGS AF: 0.402 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		0.29
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: rs16854453; hg19: chr3-169559234;