3-8403337-A-G

Variant names:

• chr3-8403337-A-G
• rs359027
• ENST00000420095.2:n.584+91344T>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+91344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 151,956 control chromosomes in the GnomAD database, including 44,473 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 0.76 (44473 hom., cov: 31)
• Consequence: LMCD1-AS1 ENST00000420095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 4 publications found

Genes affected

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

ENSG00000231401 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMCD1-AS1	NR_033378.1	n.574+91344T>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.584+91344T>C		intron_variant	Intron 3 of 3	2
LMCD1-AS1	ENST00000446281.5	n.514+91344T>C		intron_variant	Intron 3 of 5	5
LMCD1-AS1	ENST00000452802.6	n.582+91344T>C		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115981 AN: 151838 Hom.: 44443 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.764 AC: 116069 AN: 151956 Hom.: 44473 Cov.: 31 AF XY: 0.760 AC XY: 56434 AN XY: 74258

African (AFR) AF: 0.800 AC: 33131 AN: 41430

American (AMR) AF: 0.710 AC: 10833 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2616 AN: 3472

East Asian (EAS) AF: 0.605 AC: 3113 AN: 5148

South Asian (SAS) AF: 0.704 AC: 3389 AN: 4812

European-Finnish (FIN) AF: 0.741 AC: 7803 AN: 10528

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

European-Non Finnish (NFE) AF: 0.774 AC: 52650 AN: 67990

Other (OTH) AF: 0.764 AC: 1613 AN: 2110

Alfa AF: 0.775 Hom.: 6761

Bravo AF: 0.765

Asia WGS AF: 0.651 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.34
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs359027; hg19: chr3-8445023;