rs359027

Positions:

• chr3-8403337-A-G
• chr3-8403337-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033378.1(LMCD1-AS1):​n.574+91344T>C variant causes a intron, non coding transcript 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 NR_033378.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LMCD1-AS1	NR_033378.1	n.574+91344T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMCD1-AS1	ENST00000654635.1	n.588+91344T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.764

Alfa AF: 0.774 Hom.: 6513

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs359027; hg19: chr3-8445023;