Genetic Variant ENSG00000288640:n.*563A>C (chr7-112489954-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000676282.1(ENSG00000288640):n.*563A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,610,028 control chromosomes in the GnomAD database, including 237,784 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 0.45 ( 17645 hom., cov: 32)

Exomes 𝑓: 0.54 ( 220139 hom. )

Consequence

ENSG00000288640
ENST00000676282.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.946

Publications

10 publications found

Variant links:

Genes affected

ENSG00000288640 (HGNC:):

ENSG00000288640 links:

LSMEM1 (HGNC:22036): (leucine rich single-pass membrane protein 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LSMEM1 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSMEM1	NM_182597.3 link	c.*5A>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000312849.4	NP_872403.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ENSG00000288640	ENST00000676282.1 link	n.*563A>C	non_coding_transcript_exon_variant	Exon 15 of 15			ENSP00000501830.1
LSMEM1	ENST00000312849.4 link	c.*5A>C	3_prime_UTR_variant	Exon 4 of 4	1	NM_182597.3	ENSP00000323304.3
ENSG00000288640	ENST00000676282.1 link	n.*563A>C	3_prime_UTR_variant	Exon 15 of 15			ENSP00000501830.1

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

68562

AN:

151942

Hom.:

17653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.798

Gnomad AMR

AF:

0.368

Gnomad ASJ

AF:

0.631

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.628

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.495

GnomAD2 exomes

AF:

0.461

AC:

114358

AN:

247828

AF XY:

0.473

show subpopulations

Gnomad AFR exome

AF:

0.241

Gnomad AMR exome

AF:

0.252

Gnomad ASJ exome

AF:

0.632

Gnomad EAS exome

AF:

0.169

Gnomad FIN exome

AF:

0.630

Gnomad NFE exome

AF:

0.588

Gnomad OTH exome

AF:

0.511

GnomAD4 exome

AF:

0.536

AC:

781402

AN:

1457970

Hom.:

220139

Cov.:

AF XY:

0.533

AC XY:

386656

AN XY:

725322

show subpopulations

African (AFR)

AF:

0.234

AC:

7771

AN:

33192

American (AMR)

AF:

0.265

AC:

11663

AN:

43972

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

16356

AN:

25908

East Asian (EAS)

AF:

0.131

AC:

5186

AN:

39634

South Asian (SAS)

AF:

0.340

AC:

29124

AN:

85690

European-Finnish (FIN)

AF:

0.625

AC:

33181

AN:

53102

Middle Eastern (MID)

AF:

0.580

AC:

3330

AN:

5740

European-Non Finnish (NFE)

AF:

0.580

AC:

643856

AN:

1110524

Other (OTH)

AF:

0.514

AC:

30935

AN:

60208

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

17076

34152

51229

68305

85381

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17274

34548

51822

69096

86370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.451

AC:

68568

AN:

152058

Hom.:

17645

Cov.:

AF XY:

0.449

AC XY:

33390

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.245

AC:

10159

AN:

41466

American (AMR)

AF:

0.367

AC:

5612

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

2191

AN:

3470

East Asian (EAS)

AF:

0.167

AC:

865

AN:

5180

South Asian (SAS)

AF:

0.320

AC:

1545

AN:

4824

European-Finnish (FIN)

AF:

0.628

AC:

6633

AN:

10566

Middle Eastern (MID)

AF:

0.605

AC:

178

AN:

294

European-Non Finnish (NFE)

AF:

0.583

AC:

39618

AN:

67960

Other (OTH)

AF:

0.494

AC:

1041

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1717

3435

5152

6870

8587

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

610

1220

1830

2440

3050

<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:

0.538

Hom.:

30357

Bravo

AF:

0.423

Asia WGS

AF:

0.260

AC:

906

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.11

(source)

DANN

Benign

0.46

PhyloP100

-0.95

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over