rs11210404

Positions:

• chr1-74072568-G-A
• chr1-74072568-G-C
• chr1-74072568-G-T

Variant summary

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

The NM_001105659.2(LRRIQ3):​c.997+2093C>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 151,518 control chromosomes in the GnomAD database, including 19,352 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 (19352 hom., cov: 30)
• Consequence: LRRIQ3 NM_001105659.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRIQ3	NM_001105659.2	c.997+2093C>T		intron_variant		ENST00000354431.9	NP_001099129.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRIQ3	ENST00000354431.9	c.997+2093C>T		intron_variant		5	NM_001105659.2	ENSP00000346414	P2
LRRIQ3	ENST00000395089.5	c.997+2093C>T		intron_variant		5		ENSP00000378524	P2
LRRIQ3	ENST00000417067.5	c.130+2093C>T		intron_variant		2		ENSP00000390376
LRRIQ3	ENST00000415760.5	c.*2460+2093C>T		intron_variant, NMD_transcript_variant		2		ENSP00000415319

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74536 AN: 151400 Hom.: 19343 Cov.: 30

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.492 AC: 74583 AN: 151518 Hom.: 19352 Cov.: 30 AF XY: 0.497 AC XY: 36795 AN XY: 73998

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.481

Alfa AF: 0.485 Hom.: 2193

Bravo AF: 0.482

Asia WGS AF: 0.688 AC: 2390 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.68

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: rs11210404; hg19: chr1-74538252;