NM_024727.4:c.176-370C>T

Variant names:

• chr3-169862183-G-A
• rs1920116
• NM_024727.4:c.176-370C>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.176-370C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,104 control chromosomes in the GnomAD database, including 6,043 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 0.26 (6043 hom., cov: 32)
• Consequence: LRRC31 NM_024727.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 32 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC31	NM_024727.4	MANE Select	c.176-370C>T		intron	N/A	NP_079003.2
	LRRC31	NM_001277128.2		c.176-370C>T		intron	N/A	NP_001264057.1
	LRRC31	NM_001277127.2		c.176-370C>T		intron	N/A	NP_001264056.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC31	ENST00000316428.10	TSL:1 MANE Select	c.176-370C>T		intron	N/A	ENSP00000325978.5
	LRRC31	ENST00000523069.1	TSL:1	c.176-370C>T		intron	N/A	ENSP00000429145.1
	LRRC31	ENST00000945890.1		c.176-370C>T		intron	N/A	ENSP00000615949.1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39509 AN: 151986 Hom.: 6036 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.260 AC: 39526 AN: 152104 Hom.: 6043 Cov.: 32 AF XY: 0.265 AC XY: 19740 AN XY: 74360

African (AFR) AF: 0.121 AC: 5033 AN: 41536

American (AMR) AF: 0.352 AC: 5374 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 973 AN: 3472

East Asian (EAS) AF: 0.598 AC: 3091 AN: 5172

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4818

European-Finnish (FIN) AF: 0.331 AC: 3494 AN: 10546

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19243 AN: 67966

Other (OTH) AF: 0.262 AC: 552 AN: 2110

Alfa AF: 0.290 Hom.: 15457

Bravo AF: 0.260

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.81
PhyloP100		-1.3
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: rs1920116; hg19: chr3-169579971;