Genetic Variant ENSG00000228351:n.437+2824T>C (chr3-8100035-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000428171.1(ENSG00000228351):n.437+2824T>C variant causes a intron 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

ENSG00000228351
ENST00000428171.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.299

Publications

1 publications found

Variant links:

Genes affected

ENSG00000228351 (HGNC:):

ENSG00000228351 links:

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=-0.85).

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000228351	ENST00000428171.1 link	n.437+2824T>C	intron_variant	Intron 4 of 5	4
LMCD1-AS1	ENST00000446281.5 link	n.515-107733A>G	intron_variant	Intron 3 of 5	5
ENSG00000228351	ENST00000649560.2 link	n.656+2824T>C	intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes

AF:

0.573

AC:

87018

AN:

151842

Hom.:

25208

Cov.:

show subpopulations

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.:

AF XY:

0.570

AC XY:

42299

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.490

AC:

20309

AN:

41412

American (AMR)

AF:

0.564

AC:

8608

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.664

AC:

2306

AN:

3472

East Asian (EAS)

AF:

0.549

AC:

2817

AN:

5134

South Asian (SAS)

AF:

0.520

AC:

2507

AN:

4818

European-Finnish (FIN)

AF:

0.587

AC:

6212

AN:

10576

Middle Eastern (MID)

AF:

0.692

AC:

202

AN:

292

European-Non Finnish (NFE)

AF:

0.621

AC:

42216

AN:

67970

Other (OTH)

AF:

0.616

AC:

1298

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1912

3824

5735

7647

9559

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<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:

0.605

Hom.:

14225

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

(source)

DANN

Benign

0.82

PhyloP100

0.30

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