1-169736942-A-G

Variant names:

• chr1-169736942-A-G
• rs10800469
• ENST00000609271.1:c.-201-2819T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000498289.5(FIRRM):​n.852-46869A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,940 control chromosomes in the GnomAD database, including 10,472 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 0.36 (10472 hom., cov: 31)
• Consequence: FIRRM ENST00000498289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 4 publications found

Genes affected

SELE (HGNC:10718): (selectin E) The protein encoded by this gene is found in cytokine-stimulated endothelial cells and is thought to be responsible for the accumulation of blood leukocytes at sites of inflammation by mediating the adhesion of cells to the vascular lining. It exhibits structural features such as the presence of lectin- and EGF-like domains followed by short consensus repeat (SCR) domains that contain 6 conserved cysteine residues. These proteins are part of the selectin family of cell adhesion molecules. Adhesion molecules participate in the interaction between leukocytes and the endothelium and appear to be involved in the pathogenesis of atherosclerosis. [provided by RefSeq, Jul 2008]

FIRRM (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498289.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELE	ENST00000609271.1	TSL:4	c.-201-2819T>C		intron	N/A	ENSP00000476784.1
	FIRRM	ENST00000498289.5	TSL:2	n.852-46869A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54037 AN: 151822 Hom.: 10434 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.356 AC: 54126 AN: 151940 Hom.: 10472 Cov.: 31 AF XY: 0.362 AC XY: 26869 AN XY: 74250

African (AFR) AF: 0.483 AC: 19975 AN: 41398

American (AMR) AF: 0.381 AC: 5815 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2895 AN: 5176

South Asian (SAS) AF: 0.450 AC: 2164 AN: 4804

European-Finnish (FIN) AF: 0.328 AC: 3457 AN: 10548

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17470 AN: 67964

Other (OTH) AF: 0.371 AC: 784 AN: 2112

Alfa AF: 0.311 Hom.: 1093

Bravo AF: 0.368

Asia WGS AF: 0.482 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10800469; hg19: chr1-169706083;