1-169691524-A-G

Variant names:

• chr1-169691524-A-G
• rs909628
• NM_000655.5:c.*260T>C

Variant summary

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

The NM_000655.5(SELL):​c.*260T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 265,124 control chromosomes in the GnomAD database, including 1,101 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 0.077 (542 hom., cov: 32)
  • Exomes 𝑓: 0.092 (559 hom.)
• Consequence: SELL NM_000655.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 16 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELL	NM_000655.5	MANE Select	c.*260T>C		3_prime_UTR	Exon 9 of 9	NP_000646.3
	SELL	NR_029467.2		n.1348T>C		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELL	ENST00000236147.6	TSL:1 MANE Select	c.*260T>C		3_prime_UTR	Exon 9 of 9	ENSP00000236147.5
	SELL	ENST00000650983.1		c.*260T>C		3_prime_UTR	Exon 9 of 9	ENSP00000498227.1
	FIRRM	ENST00000498289.5	TSL:2	n.851+7592A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11738 AN: 152086 Hom.: 541 Cov.: 32

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0726

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0834

GnomAD4 exome AF: 0.0920 AC: 10393 AN: 112920 Hom.: 559 Cov.: 0 AF XY: 0.0934 AC XY: 5220 AN XY: 55868

African (AFR) AF: 0.0384 AC: 151 AN: 3928

American (AMR) AF: 0.0569 AC: 180 AN: 3164

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 544 AN: 4760

East Asian (EAS) AF: 0.0253 AC: 280 AN: 11052

South Asian (SAS) AF: 0.0731 AC: 80 AN: 1094

European-Finnish (FIN) AF: 0.0771 AC: 577 AN: 7482

Middle Eastern (MID) AF: 0.102 AC: 168 AN: 1646

European-Non Finnish (NFE) AF: 0.107 AC: 7687 AN: 71820

Other (OTH) AF: 0.0910 AC: 726 AN: 7974

GnomAD4 genome AF: 0.0771 AC: 11741 AN: 152204 Hom.: 542 Cov.: 32 AF XY: 0.0749 AC XY: 5575 AN XY: 74430

African (AFR) AF: 0.0398 AC: 1653 AN: 41536

American (AMR) AF: 0.0641 AC: 980 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3468

East Asian (EAS) AF: 0.00830 AC: 43 AN: 5182

South Asian (SAS) AF: 0.0727 AC: 351 AN: 4830

European-Finnish (FIN) AF: 0.0721 AC: 764 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7231 AN: 67982

Other (OTH) AF: 0.0816 AC: 172 AN: 2108

Alfa AF: 0.0903 Hom.: 554

Bravo AF: 0.0740

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.65
PhyloP100		-1.2
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: rs909628; hg19: chr1-169660665;