NM_001080460.3:c.1021-895G>T

Variant names:

• chr3-169827864-G-T
• rs10936603
• NM_001080460.3:c.1021-895G>T

Variant summary

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

The NM_001080460.3(LRRIQ4):​c.1021-895G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,960 control chromosomes in the GnomAD database, including 6,061 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 0.27 (6061 hom., cov: 32)
• Consequence: LRRIQ4 NM_001080460.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

Genes affected

LRRIQ4 (HGNC:34298): (leucine rich repeats and IQ motif containing 4) Predicted to enable protein serine/threonine phosphatase activity. Predicted to be involved in signal transduction. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRIQ4	NM_001080460.3	c.1021-895G>T		intron_variant	Intron 2 of 5	ENST00000340806.7	NP_001073929.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRIQ4	ENST00000340806.7	c.1021-895G>T		intron_variant	Intron 2 of 5	5	NM_001080460.3	ENSP00000342188.6
LRRIQ4	ENST00000691416.1	c.1021-895G>T		intron_variant	Intron 2 of 4			ENSP00000508855.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40886 AN: 151842 Hom.: 6050 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.269 AC: 40912 AN: 151960 Hom.: 6061 Cov.: 32 AF XY: 0.271 AC XY: 20141 AN XY: 74270

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.265

Alfa AF: 0.242 Hom.: 4071

Bravo AF: 0.276

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.67

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: rs10936603; hg19: chr3-169545652;