12-122170805-T-G

Variant names:

• chr12-122170805-T-G
• rs4758680
• NM_152759.5:c.-406+3023T>G

Variant summary

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

The NM_152759.5(LRRC43):​c.-406+3023T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,436 control chromosomes in the GnomAD database, including 35,156 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 0.68 (35156 hom., cov: 27)
• Consequence: LRRC43 NM_152759.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

LRRC43 (HGNC:28562): (leucine rich repeat containing 43)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC43	NM_152759.5	c.-406+3023T>G		intron_variant	Intron 1 of 11		NP_689972.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC43	ENST00000537729.5	c.-406+3023T>G		intron_variant	Intron 1 of 5	5		ENSP00000438751.1

Frequencies

GnomAD3 genomes AF: 0.680 AC: 102897 AN: 151316 Hom.: 35144 Cov.: 27

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.680 AC: 102960 AN: 151436 Hom.: 35156 Cov.: 27 AF XY: 0.681 AC XY: 50337 AN XY: 73946

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.683

Alfa AF: 0.611 Hom.: 3674

Bravo AF: 0.687

Asia WGS AF: 0.717 AC: 2497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4758680; hg19: chr12-122655352;