1-74077243-T-C

Variant names:

• chr1-74077243-T-C
• rs1483795
• NM_001105659.2:c.868-2453A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001105659.2(LRRIQ3):​c.868-2453A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 150,910 control chromosomes in the GnomAD database, including 17,894 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 0.46 (17894 hom., cov: 32)
• Consequence: LRRIQ3 NM_001105659.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105659.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRIQ3	NM_001105659.2	MANE Select	c.868-2453A>G		intron	N/A	NP_001099129.1	A6PVS8-1
	LRRIQ3	NM_001322315.2		c.868-2453A>G		intron	N/A	NP_001309244.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRIQ3	ENST00000354431.9	TSL:5 MANE Select	c.868-2453A>G		intron	N/A	ENSP00000346414.4	A6PVS8-1
	LRRIQ3	ENST00000395089.5	TSL:5	c.868-2453A>G		intron	N/A	ENSP00000378524.1	A6PVS8-1
	LRRIQ3	ENST00000415760.5	TSL:2	n.*2330+1412A>G		intron	N/A	ENSP00000415319.1	A6PVS8-2

Frequencies

GnomAD3 genomes AF: 0.464 AC: 69911 AN: 150804 Hom.: 17893 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.463 AC: 69922 AN: 150910 Hom.: 17894 Cov.: 32 AF XY: 0.469 AC XY: 34530 AN XY: 73670

African (AFR) AF: 0.240 AC: 9834 AN: 40962

American (AMR) AF: 0.485 AC: 7361 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2207 AN: 3460

East Asian (EAS) AF: 0.818 AC: 4191 AN: 5124

South Asian (SAS) AF: 0.660 AC: 3169 AN: 4802

European-Finnish (FIN) AF: 0.538 AC: 5644 AN: 10488

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.530 AC: 35816 AN: 67584

Other (OTH) AF: 0.464 AC: 974 AN: 2100

Alfa AF: 0.462 Hom.: 2594

Bravo AF: 0.450

Asia WGS AF: 0.677 AC: 2355 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1483795; hg19: chr1-74542927;