ENST00000446281.5:n.515-130729C>T

Variant names:

• chr3-8123031-G-A
• rs1878175
• ENST00000446281.5:n.515-130729C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446281.5(LMCD1-AS1):​n.515-130729C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,134 control chromosomes in the GnomAD database, including 50,921 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 0.81 (50921 hom., cov: 32)
• Consequence: LMCD1-AS1 ENST00000446281.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 2 publications found

Genes affected

LMCD1-AS1 (HGNC:44477): (LMCD1 antisense RNA 1)

ENSG00000228351 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMCD1-AS1	ENST00000446281.5	n.515-130729C>T		intron_variant	Intron 3 of 5	5
ENSG00000228351	ENST00000649560.2	n.1262+246G>A		intron_variant	Intron 9 of 9
LMCD1-AS1	ENST00000654635.1	n.746+71885C>T		intron_variant	Intron 4 of 6
LMCD1-AS1	ENST00000659617.1	n.754+71885C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123528 AN: 152016 Hom.: 50904 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.812 AC: 123589 AN: 152134 Hom.: 50921 Cov.: 32 AF XY: 0.811 AC XY: 60342 AN XY: 74380

African (AFR) AF: 0.669 AC: 27733 AN: 41458

American (AMR) AF: 0.841 AC: 12860 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3233 AN: 3472

East Asian (EAS) AF: 0.771 AC: 3991 AN: 5174

South Asian (SAS) AF: 0.723 AC: 3479 AN: 4810

European-Finnish (FIN) AF: 0.887 AC: 9391 AN: 10590

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 60016 AN: 68008

Other (OTH) AF: 0.830 AC: 1757 AN: 2116

Alfa AF: 0.855 Hom.: 139695

Bravo AF: 0.806

Asia WGS AF: 0.713 AC: 2477 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1878175; hg19: chr3-8164718;