rs1038990

Variant names:

• chr2-237638749-C-T
• rs1038990
• NM_001137550.2:c.96+11009C>T

Variant summary

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

The NM_001137550.2(LRRFIP1):​c.96+11009C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,130 control chromosomes in the GnomAD database, including 5,278 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 0.26 (5278 hom., cov: 33)
• Consequence: LRRFIP1 NM_001137550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 2 publications found

Genes affected

LRRFIP1 (HGNC:6702): (LRR binding FLII interacting protein 1) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein homodimerization activity. Involved in negative regulation of transcription by RNA polymerase II. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LRRFIP1 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001137550.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRFIP1	NM_001137550.2	MANE Select	c.96+11009C>T		intron	N/A	NP_001131022.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRFIP1	ENST00000308482.14	TSL:1 MANE Select	c.96+11009C>T		intron	N/A	ENSP00000310109.9
	LRRFIP1	ENST00000465870.5	TSL:3	n.134+11009C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38839 AN: 152010 Hom.: 5260 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.256 AC: 38890 AN: 152130 Hom.: 5278 Cov.: 33 AF XY: 0.259 AC XY: 19247 AN XY: 74354

African (AFR) AF: 0.231 AC: 9588 AN: 41494

American (AMR) AF: 0.333 AC: 5094 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 772 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2233 AN: 5170

South Asian (SAS) AF: 0.329 AC: 1584 AN: 4820

European-Finnish (FIN) AF: 0.195 AC: 2064 AN: 10582

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16587 AN: 67988

Other (OTH) AF: 0.236 AC: 499 AN: 2110

Alfa AF: 0.251 Hom.: 2837

Bravo AF: 0.261

Asia WGS AF: 0.408 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.029
DANN	Benign	0.52
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1038990; hg19: chr2-238547392;