rs10789387

chr1-74094727-G-Achr1-74094727-G-C

Variant summary

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

The NM_001105659.2(LRRIQ3):c.867+14667C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,890 control chromosomes in the GnomAD database, including 19,396 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 0.49 (19396 hom., cov: 31)
• Consequence: LRRIQ3 NM_001105659.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRIQ3	NM_001105659.2	c.867+14667C>T		intron_variant		ENST00000354431.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRIQ3	ENST00000354431.9	c.867+14667C>T		intron_variant		5	NM_001105659.2	P2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74681 AN: 151772 Hom.: 19387 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.492 AC: 74728 AN: 151890 Hom.: 19396 Cov.: 31 AF XY: 0.497 AC XY: 36873 AN XY: 74216

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.483

Alfa AF: 0.532 Hom.: 43949

Bravo AF: 0.482

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.29
Dann	Benign	0.35

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: rs10789387; hg19: chr1-74560411;