Genetic Variant NM_016357.5:c.*720T>C (chr12-50176344-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 NM_016357.5(LIMA1):c.*720T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,124 control chromosomes in the GnomAD database, including 7,168 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 0.29 ( 7167 hom., cov: 32)

Exomes 𝑓: 0.21 ( 1 hom. )

Consequence

LIMA1
NM_016357.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.771

Publications

19 publications found

Variant links:

Genes affected

LIMA1 (HGNC:24636): (LIM domain and actin binding 1) This gene encodes a cytoskeleton-associated protein that inhibits actin filament depolymerization and cross-links filaments in bundles. It is downregulated in some cancer cell lines. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and expression of some of the variants maybe independently regulated. [provided by RefSeq, Aug 2011]

LIMA1 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016357.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LIMA1	NM_016357.5	MANE Select	c.*720T>C	3_prime_UTR	Exon 11 of 11	NP_057441.1	Q9UHB6-1
LIMA1	NM_001113546.2		c.*720T>C	3_prime_UTR	Exon 11 of 11	NP_001107018.1	Q9UHB6-4
LIMA1	NM_001394886.1		c.*720T>C	3_prime_UTR	Exon 11 of 11	NP_001381815.1	Q9UHB6-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LIMA1	ENST00000341247.9	TSL:1 MANE Select	c.*720T>C	3_prime_UTR	Exon 11 of 11	ENSP00000340184.4	Q9UHB6-1
LIMA1	ENST00000394943.7	TSL:1	c.*720T>C	3_prime_UTR	Exon 11 of 11	ENSP00000378400.3	Q9UHB6-4
LIMA1	ENST00000552783.5	TSL:1	c.*720T>C	3_prime_UTR	Exon 8 of 8	ENSP00000448779.1	Q9UHB6-5

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44725

AN:

151992

Hom.:

7173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.0104

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.291

GnomAD4 exome

AF:

0.214

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.825

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.294

AC:

44716

AN:

152110

Hom.:

7167

Cov.:

AF XY:

0.286

AC XY:

21240

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.248

AC:

10304

AN:

41504

American (AMR)

AF:

0.209

AC:

3190

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

718

AN:

3464

East Asian (EAS)

AF:

0.0106

AC:

AN:

5188

South Asian (SAS)

AF:

0.365

AC:

1760

AN:

4826

European-Finnish (FIN)

AF:

0.275

AC:

2908

AN:

10558

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.365

AC:

24833

AN:

67978

Other (OTH)

AF:

0.288

AC:

607

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1560

3120

4680

6240

7800

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.328

Hom.:

22170

Bravo

AF:

0.283

Asia WGS

AF:

0.205

AC:

715

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.7

(source)

DANN

Benign

0.65

PhyloP100

0.77

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over