chr3-8209103-A-C

Variant names:

• chr3-8209103-A-C
• rs9866825
• ENST00000446281.5:n.515-216801T>G

Variant summary

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

The ENST00000446281.5(LMCD1-AS1):​n.515-216801T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,016 control chromosomes in the GnomAD database, including 24,403 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 0.56 (24403 hom., cov: 32)
• Consequence: LMCD1-AS1 ENST00000446281.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LMCD1-AS1	ENST00000446281.5	TSL:5	n.515-216801T>G		intron	N/A
	LMCD1-AS1	ENST00000452802.6	TSL:2	n.583-14030T>G		intron	N/A
	LMCD1-AS1	ENST00000654635.1		n.589-14030T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85663 AN: 151898 Hom.: 24371 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.564 AC: 85743 AN: 152016 Hom.: 24403 Cov.: 32 AF XY: 0.569 AC XY: 42254 AN XY: 74304

African (AFR) AF: 0.598 AC: 24792 AN: 41464

American (AMR) AF: 0.527 AC: 8038 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1656 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3917 AN: 5170

South Asian (SAS) AF: 0.676 AC: 3255 AN: 4818

European-Finnish (FIN) AF: 0.589 AC: 6205 AN: 10538

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35988 AN: 67974

Other (OTH) AF: 0.560 AC: 1182 AN: 2112

Alfa AF: 0.558 Hom.: 8018

Bravo AF: 0.561

Asia WGS AF: 0.744 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.49
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs9866825; hg19: chr3-8250790;