3-8153989-A-G

Position:

• chr3-8153989-A-G

Variant summary

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

The ENST00000654635.1(LMCD1-AS1):​n.746+40927T>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 0.141 in 152,082 control chromosomes in the GnomAD database, including 1,961 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 0.14 (1961 hom., cov: 32)
• Consequence: LMCD1-AS1 ENST00000654635.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMCD1-AS1	ENST00000654635.1	n.746+40927T>C		intron_variant, non_coding_transcript_variant
LMCD1-AS1	ENST00000446281.5	n.515-161687T>C		intron_variant, non_coding_transcript_variant		5
LMCD1-AS1	ENST00000659617.1	n.754+40927T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21459 AN: 151964 Hom.: 1957 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.0996

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.141 AC: 21484 AN: 152082 Hom.: 1961 Cov.: 32 AF XY: 0.143 AC XY: 10651 AN XY: 74350

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.0996

Gnomad4 NFE AF: 0.0839

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0913 Hom.: 1265

Bravo AF: 0.143

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.49
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6796806; hg19: chr3-8195676;