rs1038990

chr2-237638749-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRFIP1	NM_001137550.2	c.96+11009C>T		intron_variant		ENST00000308482.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRFIP1	ENST00000308482.14	c.96+11009C>T		intron_variant		1	NM_001137550.2	P1
LRRFIP1	ENST00000465870.5	n.134+11009C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.236

Alfa AF: 0.253 Hom.: 2621

Bravo AF: 0.261

Asia WGS AF: 0.408 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.029
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1038990; hg19: chr2-238547392;