1-169691524-A-G

Position:

• chr1-169691524-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELL	NM_000655.5	c.*260T>C		3_prime_UTR_variant	9/9	ENST00000236147.6	NP_000646.3
SELL	NR_029467.2	n.1348T>C		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELL	ENST00000236147.6	c.*260T>C		3_prime_UTR_variant	9/9	1	NM_000655.5	ENSP00000236147	P1
SELL	ENST00000650983.1	c.*260T>C		3_prime_UTR_variant	9/9			ENSP00000498227
FIRRM	ENST00000498289.5	n.851+7592A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR exome AF: 0.0384

Gnomad4 AMR exome AF: 0.0569

Gnomad4 ASJ exome AF: 0.114

Gnomad4 EAS exome AF: 0.0253

Gnomad4 SAS exome AF: 0.0731

Gnomad4 FIN exome AF: 0.0771

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.0910

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

Gnomad4 AFR AF: 0.0398

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.00830

Gnomad4 SAS AF: 0.0727

Gnomad4 FIN AF: 0.0721

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0816

Alfa AF: 0.0932 Hom.: 399

Bravo AF: 0.0740

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.65

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: rs909628; hg19: chr1-169660665;