rs408070

Variant names:

• chr8-81280412-G-A
• rs408070
• ENST00000517670.2:n.242-36C>T

Variant summary

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

The ENST00000517670.2(LNMICC):​n.242-36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000981 in 1,120,804 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000098 (0 hom.)
• Consequence: LNMICC ENST00000517670.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796
• Publications: 1 publications found

Genes affected

LNMICC (HGNC:56001): (lncRNA associated with lymph node metastasis in cervical cancer)

FABP5 (HGNC:3560): (fatty acid binding protein 5) This gene encodes the fatty acid binding protein found in epidermal cells, and was first identified as being upregulated in psoriasis tissue. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. FABPs may play roles in fatty acid uptake, transport, and metabolism. Polymorphisms in this gene are associated with type 2 diabetes. The human genome contains many pseudogenes similar to this locus.[provided by RefSeq, Feb 2011]

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=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNMICC	NR_186603.1	n.93-36C>T		intron_variant	Intron 1 of 1
LNMICC	NR_186604.1	n.106-36C>T		intron_variant	Intron 1 of 1
FABP5	NM_001444.3	c.-184G>A		upstream_gene_variant		ENST00000297258.11	NP_001435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP5	ENST00000297258.11	c.-184G>A		upstream_gene_variant		1	NM_001444.3	ENSP00000297258.6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000981 AC: 11 AN: 1120804 Hom.: 0 Cov.: 30 AF XY: 0.00000559 AC XY: 3 AN XY: 536518

African (AFR) AF: 0.00 AC: 0 AN: 22126

American (AMR) AF: 0.00 AC: 0 AN: 7770

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14244

East Asian (EAS) AF: 0.0000407 AC: 1 AN: 24600

South Asian (SAS) AF: 0.00 AC: 0 AN: 33384

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24240

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2994

European-Non Finnish (NFE) AF: 0.0000106 AC: 10 AN: 946424

Other (OTH) AF: 0.00 AC: 0 AN: 45022

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.6
DANN	Benign	0.89
PhyloP100		-0.80
PromoterAI		-0.061	Neutral

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: rs408070; hg19: chr8-82192647;