1-169736942-A-G

Variant names:

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

Variant summary

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

The ENST00000609271.1(SELE):​c.-201-2819T>C 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: SELE ENST00000609271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

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]

C1orf112 (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000609271.1	c.-201-2819T>C		intron_variant	Intron 1 of 2	4		ENSP00000476784.1
C1orf112	ENST00000498289.5	n.852-46869A>G		intron_variant	Intron 3 of 28	2

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

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.371

Alfa AF: 0.304 Hom.: 1006

Bravo AF: 0.368

Asia WGS AF: 0.482 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10800469; hg19: chr1-169706083;