ENST00000420095.2:n.585-96702A>C

Variant names:

• chr3-8319421-T-G
• rs6766972
• ENST00000420095.2:n.585-96702A>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.585-96702A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,054 control chromosomes in the GnomAD database, including 40,397 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 0.72 (40397 hom., cov: 32)
• Consequence: LMCD1-AS1 ENST00000420095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 0 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 (NFE) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMCD1-AS1	NR_033378.1	n.575-96702A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMCD1-AS1	ENST00000420095.2	n.585-96702A>C		intron_variant	Intron 3 of 3	2
LMCD1-AS1	ENST00000446281.5	n.514+175260A>C		intron_variant	Intron 3 of 5	5
LMCD1-AS1	ENST00000452802.6	n.583-124348A>C		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109992 AN: 151936 Hom.: 40355 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.724 AC: 110083 AN: 152054 Hom.: 40397 Cov.: 32 AF XY: 0.722 AC XY: 53648 AN XY: 74316

African (AFR) AF: 0.615 AC: 25491 AN: 41452

American (AMR) AF: 0.706 AC: 10779 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2495 AN: 3472

East Asian (EAS) AF: 0.669 AC: 3439 AN: 5142

South Asian (SAS) AF: 0.650 AC: 3128 AN: 4814

European-Finnish (FIN) AF: 0.798 AC: 8456 AN: 10590

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53904 AN: 67994

Other (OTH) AF: 0.725 AC: 1532 AN: 2114

Alfa AF: 0.701 Hom.: 8684

Bravo AF: 0.713

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs6766972; hg19: chr3-8361109;