1-110914865-T-G

Position:

• chr1-110914865-T-G

Variant summary

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

The XM_017001769.3(LRIF1):​c.1869+34986A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,052 control chromosomes in the GnomAD database, including 16,081 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 0.45 (16081 hom., cov: 32)
• Consequence: LRIF1 XM_017001769.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

LRIF1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRIF1	XM_017001769.3	c.1869+34986A>C		intron_variant			XP_016857258.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69098 AN: 151934 Hom.: 16077 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.455 AC: 69121 AN: 152052 Hom.: 16081 Cov.: 32 AF XY: 0.458 AC XY: 34054 AN XY: 74346

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.429

Alfa AF: 0.464 Hom.: 8261

Bravo AF: 0.452

Asia WGS AF: 0.485 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1282020; hg19: chr1-111457487;