3-8153989-A-G

Variant names:

• chr3-8153989-A-G
• rs6796806
• ENST00000446281.5:n.515-161687T>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.515-161687T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,082 control chromosomes in the GnomAD database, including 1,961 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 0.14 (1961 hom., cov: 32)
• Consequence: LMCD1-AS1 ENST00000446281.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 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.515-161687T>C		intron	N/A
	LMCD1-AS1	ENST00000654635.1		n.746+40927T>C		intron	N/A
	LMCD1-AS1	ENST00000659617.1		n.754+40927T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21459 AN: 151964 Hom.: 1957 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.141 AC: 21484 AN: 152082 Hom.: 1961 Cov.: 32 AF XY: 0.143 AC XY: 10651 AN XY: 74350

African (AFR) AF: 0.248 AC: 10266 AN: 41458

American (AMR) AF: 0.113 AC: 1723 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1056 AN: 5158

South Asian (SAS) AF: 0.251 AC: 1207 AN: 4814

European-Finnish (FIN) AF: 0.0996 AC: 1055 AN: 10588

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

European-Non Finnish (NFE) AF: 0.0839 AC: 5708 AN: 67998

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.104 Hom.: 2969

Bravo AF: 0.143

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.49
DANN	Benign	0.64
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs6796806; hg19: chr3-8195676;