ENST00000446281.5:n.515-166282T>C

Variant names:

• chr3-8158584-A-G
• rs6764798
• ENST00000446281.5:n.515-166282T>C

Variant summary

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

The ENST00000446281.5(LMCD1-AS1):​n.515-166282T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,194 control chromosomes in the GnomAD database, including 3,476 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 0.17 (3476 hom., cov: 32)
• Consequence: LMCD1-AS1 ENST00000446281.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446281.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMCD1-AS1	ENST00000446281.5	TSL:5	n.515-166282T>C		intron	N/A
	LMCD1-AS1	ENST00000654635.1		n.746+36332T>C		intron	N/A
	LMCD1-AS1	ENST00000659617.1		n.754+36332T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26333 AN: 152076 Hom.: 3463 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0838

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.173 AC: 26382 AN: 152194 Hom.: 3476 Cov.: 32 AF XY: 0.174 AC XY: 12937 AN XY: 74416

African (AFR) AF: 0.363 AC: 15036 AN: 41474

American (AMR) AF: 0.124 AC: 1901 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1049 AN: 5176

South Asian (SAS) AF: 0.234 AC: 1126 AN: 4816

European-Finnish (FIN) AF: 0.0996 AC: 1057 AN: 10614

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0838 AC: 5700 AN: 68034

Other (OTH) AF: 0.147 AC: 311 AN: 2116

Alfa AF: 0.115 Hom.: 4782

Bravo AF: 0.180

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6764798; hg19: chr3-8200271;