rs272411

Variant names:

• chr19-54600262-T-C
• rs272411
• NM_006863.4:c.1313-250T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006863.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRA1	NM_006863.4	MANE Select	c.1313-250T>C		intron	N/A	NP_006854.1	O75019-1
	LILRA1	NM_001278318.2		c.713-250T>C		intron	N/A	NP_001265247.1	O75019-2
	LILRA1	NR_103501.2		n.1313-250T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRA1	ENST00000251372.8	TSL:1 MANE Select	c.1313-250T>C		intron	N/A	ENSP00000251372.3	O75019-1
	LILRA1	ENST00000453777.1	TSL:1	c.713-250T>C		intron	N/A	ENSP00000413715.1	O75019-2
	LILRA1	ENST00000473156.5	TSL:1	n.1363-250T>C		intron	N/A

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

African (AFR) AF: 0.805 AC: 33371 AN: 41460

American (AMR) AF: 0.800 AC: 12219 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2753 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4535 AN: 5164

South Asian (SAS) AF: 0.861 AC: 4157 AN: 4826

European-Finnish (FIN) AF: 0.735 AC: 7756 AN: 10558

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48852 AN: 67980

Other (OTH) AF: 0.756 AC: 1592 AN: 2106

Alfa AF: 0.729 Hom.: 68241

Bravo AF: 0.769

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs272411; hg19: chr19-55111727;