rs2298899

Positions:

• chr1-169700591-C-T

Variant summary

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

The NM_000655.5(SELL):​c.1081+969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,202 control chromosomes in the GnomAD database, including 1,097 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 0.11 (1097 hom., cov: 31)
• Consequence: SELL NM_000655.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

SELL (HGNC:10720): (selectin L) This gene encodes a cell surface adhesion molecule that belongs to a family of adhesion/homing receptors. The encoded protein contains a C-type lectin-like domain, a calcium-binding epidermal growth factor-like domain, and two short complement-like repeats. The gene product is required for binding and subsequent rolling of leucocytes on endothelial cells, facilitating their migration into secondary lymphoid organs and inflammation sites. Single-nucleotide polymorphisms in this gene have been associated with various diseases including immunoglobulin A nephropathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2009]

C1orf112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELL	NM_000655.5	c.1081+969G>A		intron_variant		ENST00000236147.6	NP_000646.3
SELL	NR_029467.2	n.1050+969G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELL	ENST00000236147.6	c.1081+969G>A		intron_variant		1	NM_000655.5	ENSP00000236147.5
SELL	ENST00000650983.1	c.1120+969G>A		intron_variant				ENSP00000498227.1
SELL	ENST00000497295.1	c.73+2664G>A		intron_variant		5		ENSP00000498707.1
C1orf112	ENST00000498289.5	n.851+16659C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16608 AN: 152084 Hom.: 1093 Cov.: 31

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.109 AC: 16625 AN: 152202 Hom.: 1097 Cov.: 31 AF XY: 0.112 AC XY: 8299 AN XY: 74418

Gnomad4 AFR AF: 0.0758

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0824

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0959

Gnomad4 OTH AF: 0.125

Alfa AF: 0.108 Hom.: 1029

Bravo AF: 0.115

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2298899; hg19: chr1-169669732;