1-74103068-C-G

Variant summary

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

The NM_001105659.2(LRRIQ3):c.867+6326G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,758 control chromosomes in the GnomAD database, including 20,338 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 0.51 (20338 hom., cov: 31)
• Consequence: LRRIQ3 NM_001105659.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

LRRIQ3 (HGNC:28318): (leucine rich repeats and IQ motif containing 3)

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 = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRIQ3	NM_001105659.2	c.867+6326G>C		intron_variant		ENST00000354431.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRIQ3	ENST00000354431.9	c.867+6326G>C		intron_variant		5	NM_001105659.2	P2

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77010 AN: 151640 Hom.: 20325 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.508 AC: 77073 AN: 151758 Hom.: 20338 Cov.: 31 AF XY: 0.512 AC XY: 37942 AN XY: 74120

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.493

Alfa AF: 0.357 Hom.: 912

Bravo AF: 0.500

Asia WGS AF: 0.690 AC: 2401 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	0.12
Dann	Benign	0.52

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: rs10789388; hg19: chr1-74568752; COSMIC: COSV63045311;