3-8469180-C-G

Variant names:

• chr3-8469180-C-G
• rs4501099
• ENST00000420095.2:n.584+25501G>C

Variant summary

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

The ENST00000420095.2(LMCD1-AS1):​n.584+25501G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,736 control chromosomes in the GnomAD database, including 33,815 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 0.66 (33815 hom., cov: 30)
• Consequence: LMCD1-AS1 ENST00000420095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420095.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMCD1-AS1	NR_033378.1		n.574+25501G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMCD1-AS1	ENST00000420095.2	TSL:2	n.584+25501G>C		intron	N/A
	LMCD1-AS1	ENST00000446281.5	TSL:5	n.514+25501G>C		intron	N/A
	LMCD1-AS1	ENST00000452802.6	TSL:2	n.582+25501G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99608 AN: 151622 Hom.: 33780 Cov.: 30

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.657 AC: 99706 AN: 151736 Hom.: 33815 Cov.: 30 AF XY: 0.650 AC XY: 48129 AN XY: 74096

African (AFR) AF: 0.812 AC: 33591 AN: 41376

American (AMR) AF: 0.612 AC: 9343 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2111 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1476 AN: 5140

South Asian (SAS) AF: 0.550 AC: 2641 AN: 4802

European-Finnish (FIN) AF: 0.557 AC: 5816 AN: 10448

Middle Eastern (MID) AF: 0.601 AC: 173 AN: 288

European-Non Finnish (NFE) AF: 0.628 AC: 42653 AN: 67930

Other (OTH) AF: 0.663 AC: 1395 AN: 2104

Alfa AF: 0.557 Hom.: 1748

Bravo AF: 0.667

Asia WGS AF: 0.488 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.71
DANN	Benign	0.25
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4501099; hg19: chr3-8510866;