NM_000655.5:c.*144T>C

Variant names:

• chr1-169691640-A-G
• rs12938
• NM_000655.5:c.*144T>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.*144T>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 0.257 in 413,822 control chromosomes in the GnomAD database, including 14,809 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 0.27 (5715 hom., cov: 31)
  • Exomes 𝑓: 0.25 (9094 hom.)
• Consequence: SELL NM_000655.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 28 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 = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELL	NM_000655.5	c.*144T>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000236147.6	NP_000646.3
SELL	NR_029467.2	n.1232T>C		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELL	ENST00000236147.6	c.*144T>C		3_prime_UTR_variant	Exon 9 of 9	1	NM_000655.5	ENSP00000236147.5
SELL	ENST00000650983.1	c.*144T>C		3_prime_UTR_variant	Exon 9 of 9			ENSP00000498227.1
FIRRM	ENST00000498289.5	n.851+7708A>G		intron_variant	Intron 3 of 28	2
SELL	ENST00000497295.1	c.*144T>C		downstream_gene_variant		5		ENSP00000498707.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40454 AN: 151956 Hom.: 5715 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.252 AC: 65992 AN: 261750 Hom.: 9094 Cov.: 5 AF XY: 0.253 AC XY: 33258 AN XY: 131622

African (AFR) AF: 0.318 AC: 2121 AN: 6674

American (AMR) AF: 0.191 AC: 1090 AN: 5702

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 2016 AN: 8036

East Asian (EAS) AF: 0.0410 AC: 836 AN: 20382

South Asian (SAS) AF: 0.244 AC: 1192 AN: 4876

European-Finnish (FIN) AF: 0.221 AC: 6075 AN: 27524

Middle Eastern (MID) AF: 0.320 AC: 891 AN: 2788

European-Non Finnish (NFE) AF: 0.281 AC: 48026 AN: 170770

Other (OTH) AF: 0.250 AC: 3745 AN: 14998

GnomAD4 genome AF: 0.266 AC: 40458 AN: 152072 Hom.: 5715 Cov.: 31 AF XY: 0.262 AC XY: 19479 AN XY: 74352

African (AFR) AF: 0.314 AC: 13018 AN: 41444

American (AMR) AF: 0.206 AC: 3155 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 844 AN: 3462

East Asian (EAS) AF: 0.0606 AC: 314 AN: 5180

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4822

European-Finnish (FIN) AF: 0.228 AC: 2419 AN: 10590

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18767 AN: 67980

Other (OTH) AF: 0.254 AC: 535 AN: 2108

Alfa AF: 0.270 Hom.: 21986

Bravo AF: 0.265

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.43
PhyloP100		-2.7
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: rs12938; hg19: chr1-169660781; COSMIC: COSV52550651; COSMIC: COSV52550651;