rs4987361

Variant names:

• chr1-169695241-G-C
• rs4987361
• NM_000655.5:c.1100+1294C>G

Variant summary

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

The NM_000655.5(SELL):​c.1100+1294C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,188 control chromosomes in the GnomAD database, including 1,624 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 (1624 hom., cov: 32)
• Consequence: SELL NM_000655.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000655.5. 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
	SELL	NM_000655.5	MANE Select	c.1100+1294C>G		intron	N/A	NP_000646.3	P14151-1
	SELL	NR_029467.2		n.1069+1294C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELL	ENST00000236147.6	TSL:1 MANE Select	c.1100+1294C>G		intron	N/A	ENSP00000236147.5	P14151-1
	SELL	ENST00000650983.1		c.1139+1294C>G		intron	N/A	ENSP00000498227.1	P14151-2
	SELL	ENST00000878074.1		c.1100+1294C>G		intron	N/A	ENSP00000548133.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16056 AN: 152070 Hom.: 1615 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.0998

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

GnomAD4 genome AF: 0.106 AC: 16097 AN: 152188 Hom.: 1624 Cov.: 32 AF XY: 0.104 AC XY: 7776 AN XY: 74418

African (AFR) AF: 0.261 AC: 10853 AN: 41506

American (AMR) AF: 0.0594 AC: 909 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3472

East Asian (EAS) AF: 0.0415 AC: 215 AN: 5176

South Asian (SAS) AF: 0.0953 AC: 460 AN: 4828

European-Finnish (FIN) AF: 0.0350 AC: 371 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2755 AN: 67986

Other (OTH) AF: 0.104 AC: 221 AN: 2116

Alfa AF: 0.0740 Hom.: 120

Bravo AF: 0.115

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.38
PhyloP100		0.58
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: rs4987361; hg19: chr1-169664382;