NM_001137550.2:c.96+16590C>T

Variant names:

• chr2-237644330-C-T
• rs11895665
• NM_001137550.2:c.96+16590C>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+16590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,208 control chromosomes in the GnomAD database, including 1,977 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 0.14 (1977 hom., cov: 33)
• Consequence: LRRFIP1 NM_001137550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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+16590C>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+16590C>T		intron	N/A	ENSP00000310109.9
	LRRFIP1	ENST00000465870.5	TSL:3	n.134+16590C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21454 AN: 152090 Hom.: 1966 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.141 AC: 21492 AN: 152208 Hom.: 1977 Cov.: 33 AF XY: 0.141 AC XY: 10509 AN XY: 74442

African (AFR) AF: 0.261 AC: 10823 AN: 41522

American (AMR) AF: 0.109 AC: 1665 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5170

South Asian (SAS) AF: 0.103 AC: 498 AN: 4826

European-Finnish (FIN) AF: 0.0948 AC: 1005 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0845 AC: 5745 AN: 68006

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.102 Hom.: 4128

Bravo AF: 0.149

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.6
DANN	Benign	0.27
PhyloP100		0.15
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: rs11895665; hg19: chr2-238552973;