3-8100035-T-C

Variant summary

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

The ENST00000649560.2(ENSG00000228351):n.656+2824T>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 0.573 in 151,960 control chromosomes in the GnomAD database, including 25,228 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 0.57 (25228 hom., cov: 32)
• Consequence: ENST00000649560.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

(HGNC:):

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649560.2	n.656+2824T>C		intron_variant, non_coding_transcript_variant
LMCD1-AS1	ENST00000654635.1	n.746+94881A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87018 AN: 151842 Hom.: 25208 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.573 AC: 87077 AN: 151960 Hom.: 25228 Cov.: 32 AF XY: 0.570 AC XY: 42299 AN XY: 74258

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.616

Alfa AF: 0.605 Hom.: 12099

Bravo AF: 0.567

Asia WGS AF: 0.528 AC: 1834 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.8
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9852802; hg19: chr3-8141722;