rs454550

Variant names:

• chr8-81279417-G-C
• rs454550
• NR_186603.1:n.1052C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_186603.1(LNMICC):​n.1052C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0264 in 152,234 control chromosomes in the GnomAD database, including 72 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 0.026 (72 hom., cov: 31)
• Consequence: LNMICC NR_186603.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0264 (4017/152234) while in subpopulation NFE AF = 0.0387 (2634/68010). AF 95% confidence interval is 0.0375. There are 72 homozygotes in GnomAd4. There are 1948 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 72 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNMICC	NR_186603.1	n.1052C>G		non_coding_transcript_exon_variant	Exon 2 of 2
LNMICC	NR_186604.1	n.1065C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNMICC	ENST00000720861.1	n.89+1916C>G		intron_variant	Intron 1 of 1
LNMICC	ENST00000720862.1	n.737+225C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 4016 AN: 152116 Hom.: 72 Cov.: 31

Gnomad AFR AF: 0.00715

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00871

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0402

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0264 AC: 4017 AN: 152234 Hom.: 72 Cov.: 31 AF XY: 0.0262 AC XY: 1948 AN XY: 74442

African (AFR) AF: 0.00713 AC: 296 AN: 41532

American (AMR) AF: 0.0374 AC: 573 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.00913 AC: 44 AN: 4820

European-Finnish (FIN) AF: 0.0136 AC: 144 AN: 10608

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0387 AC: 2634 AN: 68010

Other (OTH) AF: 0.0402 AC: 85 AN: 2112

Alfa AF: 0.0310 Hom.: 9

Bravo AF: 0.0272

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.73
PhyloP100		1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs454550; hg19: chr8-82191652;