3-169852453-A-C

Position:

• chr3-169852453-A-C

Variant summary

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

The NM_024727.4(LRRC31):​c.992-667T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 150,640 control chromosomes in the GnomAD database, including 6,900 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 0.29 (6900 hom., cov: 30)
• Consequence: LRRC31 NM_024727.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

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 = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC31	NM_024727.4	c.992-667T>G		intron_variant		ENST00000316428.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC31	ENST00000316428.10	c.992-667T>G		intron_variant		1	NM_024727.4	P1
LRRC31	ENST00000523069.1	c.992-667T>G		intron_variant		1
LRRC31	ENST00000264676.9	c.824-667T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43266 AN: 150536 Hom.: 6892 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.287 AC: 43289 AN: 150640 Hom.: 6900 Cov.: 30 AF XY: 0.293 AC XY: 21496 AN XY: 73474

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.281

Alfa AF: 0.288 Hom.: 9398

Bravo AF: 0.292

Asia WGS AF: 0.415 AC: 1403 AN: 3382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.36

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: rs11709840; hg19: chr3-169570241;