rs272411

Positions:

• chr19-54600262-T-C

Variant summary

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

The NM_006863.4(LILRA1):​c.1313-250T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,052 control chromosomes in the GnomAD database, including 44,495 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 0.76 (44495 hom., cov: 31)
• Consequence: LILRA1 NM_006863.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

Genes affected

LILRA1 (HGNC:6602): (leukocyte immunoglobulin like receptor A1) This gene encodes an activating member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein is predominantly expressed in B cells, interacts with major histocompatibility complex class I ligands, and contributes to the regulation of immune responses. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LILRA1	NM_006863.4	c.1313-250T>C		intron_variant		ENST00000251372.8
LILRA1	NM_001278318.2	c.713-250T>C		intron_variant
LILRA1	NR_103501.2	n.1313-250T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LILRA1	ENST00000251372.8	c.1313-250T>C		intron_variant		1	NM_006863.4	P1
LILRA1	ENST00000453777.1	c.713-250T>C		intron_variant		1
LILRA1	ENST00000473156.5	n.1363-250T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115957 AN: 151934 Hom.: 44450 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.763 AC: 116063 AN: 152052 Hom.: 44495 Cov.: 31 AF XY: 0.766 AC XY: 56944 AN XY: 74308

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.756

Alfa AF: 0.722 Hom.: 40089

Bravo AF: 0.769

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs272411; hg19: chr19-55111727;