rs2298902

Variant names:

• chr1-169693938-G-T
• rs2298902
• NM_000655.5:c.1101-2136C>A

Variant summary

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

The NM_000655.5(SELL):​c.1101-2136C>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 152,214 control chromosomes in the GnomAD database, including 1,041 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 (1041 hom., cov: 32)
• Consequence: SELL NM_000655.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 7 publications found

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]

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELL	NM_000655.5	c.1101-2136C>A		intron_variant	Intron 8 of 8	ENST00000236147.6	NP_000646.3
SELL	NR_029467.2	n.1070-2136C>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELL	ENST00000236147.6	c.1101-2136C>A		intron_variant	Intron 8 of 8	1	NM_000655.5	ENSP00000236147.5
SELL	ENST00000650983.1	c.1140-2136C>A		intron_variant	Intron 8 of 8			ENSP00000498227.1
SELL	ENST00000497295.1	c.93-2136C>A		intron_variant	Intron 2 of 2	5		ENSP00000498707.1
FIRRM	ENST00000498289.5	n.851+10006G>T		intron_variant	Intron 3 of 28	2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16645 AN: 152096 Hom.: 1038 Cov.: 32

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.109 AC: 16652 AN: 152214 Hom.: 1041 Cov.: 32 AF XY: 0.111 AC XY: 8264 AN XY: 74426

African (AFR) AF: 0.0817 AC: 3392 AN: 41514

American (AMR) AF: 0.139 AC: 2121 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3468

East Asian (EAS) AF: 0.134 AC: 694 AN: 5184

South Asian (SAS) AF: 0.191 AC: 921 AN: 4824

European-Finnish (FIN) AF: 0.0851 AC: 902 AN: 10604

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7574 AN: 68010

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.116 Hom.: 1700

Bravo AF: 0.111

Asia WGS AF: 0.158 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2298902; hg19: chr1-169663079;