rs11895665

chr2-237644330-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+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

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRFIP1	NM_001137550.2	c.96+16590C>T		intron_variant		ENST00000308482.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRFIP1	ENST00000308482.14	c.96+16590C>T		intron_variant		1	NM_001137550.2	P1
LRRFIP1	ENST00000465870.5	n.134+16590C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0925 Hom.: 1441

Bravo AF: 0.149

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	8.6
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11895665; hg19: chr2-238552973;