chr1-169691640-A-T

Variant names:

• chr1-169691640-A-T
• rs12938
• NM_000655.5:c.*144T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000655.5(SELL):​c.*144T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SELL NM_000655.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELL	NM_000655.5	c.*144T>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000236147.6	NP_000646.3
SELL	NR_029467.2	n.1232T>A		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>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_000655.5	ENSP00000236147.5
SELL	ENST00000650983.1	c.*144T>A		3_prime_UTR_variant	Exon 9 of 9			ENSP00000498227.1
FIRRM	ENST00000498289.5	n.851+7708A>T		intron_variant	Intron 3 of 28	2
SELL	ENST00000497295.1	c.*144T>A		downstream_gene_variant		5		ENSP00000498707.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 262518 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 132040

African (AFR) AF: 0.00 AC: 0 AN: 6692

American (AMR) AF: 0.00 AC: 0 AN: 5718

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8062

East Asian (EAS) AF: 0.00 AC: 0 AN: 20392

South Asian (SAS) AF: 0.00 AC: 0 AN: 4884

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2790

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 171356

Other (OTH) AF: 0.00 AC: 0 AN: 15028

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.13
DANN	Benign	0.66
PhyloP100		-2.7

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;