dbSNP rs6796806: LMCD1-AS1:n.515-161687T>C (chr3-8153989-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000446281.5(LMCD1-AS1):n.515-161687T>C variant causes a intron 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
ENST00000446281.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0780

Publications

1 publications found

Variant links:

Genes affected

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

LMCD1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LMCD1-AS1	ENST00000446281.5 link	n.515-161687T>C	intron_variant	Intron 3 of 5	5
LMCD1-AS1	ENST00000654635.1 link	n.746+40927T>C	intron_variant	Intron 4 of 6
LMCD1-AS1	ENST00000659617.1 link	n.754+40927T>C	intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21459

AN:

151964

Hom.:

1957

Cov.:

show subpopulations

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.:

AF XY:

0.143

AC XY:

10651

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.248

AC:

10266

AN:

41458

American (AMR)

AF:

0.113

AC:

1723

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0378

AC:

131

AN:

3468

East Asian (EAS)

AF:

0.205

AC:

1056

AN:

5158

South Asian (SAS)

AF:

0.251

AC:

1207

AN:

4814

European-Finnish (FIN)

AF:

0.0996

AC:

1055

AN:

10588

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0839

AC:

5708

AN:

67998

Other (OTH)

AF:

0.126

AC:

266

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

905

1811

2716

3622

4527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.104

Hom.:

2969

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

(source)

DANN

Benign

0.64

PhyloP100

-0.078

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over