rs1548342

Positions:

• chr1-110928432-G-A
• chr1-110928432-G-C
• chr1-110928432-G-T

Variant summary

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

The XM_017001769.3(LRIF1):​c.1869+21419C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,962 control chromosomes in the GnomAD database, including 14,278 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 0.42 (14278 hom., cov: 31)
• Consequence: LRIF1 XM_017001769.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

LRIF1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRIF1	XM_017001769.3	c.1869+21419C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63411 AN: 151842 Hom.: 14280 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.417 AC: 63421 AN: 151962 Hom.: 14278 Cov.: 31 AF XY: 0.421 AC XY: 31302 AN XY: 74266

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.401

Alfa AF: 0.434 Hom.: 2438

Bravo AF: 0.410

Asia WGS AF: 0.475 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1548342; hg19: chr1-111471054;