rs1878175

Positions:

• chr3-8123031-G-A

Variant summary

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

The ENST00000649560.2(ENSG00000228351):​n.1262+246G>A 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 0.812 in 152,134 control chromosomes in the GnomAD database, including 50,921 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 0.81 (50921 hom., cov: 32)
• Consequence: ENST00000649560.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.877 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.1262+246G>A		intron_variant, non_coding_transcript_variant
LMCD1-AS1	ENST00000654635.1	n.746+71885C>T		intron_variant, non_coding_transcript_variant
LMCD1-AS1	ENST00000446281.5	n.515-130729C>T		intron_variant, non_coding_transcript_variant		5
LMCD1-AS1	ENST00000659617.1	n.754+71885C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123528 AN: 152016 Hom.: 50904 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.812 AC: 123589 AN: 152134 Hom.: 50921 Cov.: 32 AF XY: 0.811 AC XY: 60342 AN XY: 74380

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.830

Alfa AF: 0.872 Hom.: 91691

Bravo AF: 0.806

Asia WGS AF: 0.713 AC: 2477 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878175; hg19: chr3-8164718;