Genetic Variant NM_138389.4:c.1161+143A>C (chr4-38929476-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 NM_138389.4(FAM114A1):c.1161+143A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 641,218 control chromosomes in the GnomAD database, including 23,519 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 0.24 ( 5044 hom., cov: 33)

Exomes 𝑓: 0.25 ( 18475 hom. )

Consequence

FAM114A1
NM_138389.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69

Publications

7 publications found

Variant links:

Genes affected

FAM114A1 (HGNC:25087): (family with sequence similarity 114 member A1) The protein encoded by this gene belongs to the FAM114 family and may play a role in neuronal cell development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]

FAM114A1 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM114A1	NM_138389.4 link	c.1161+143A>C		intron_variant	Intron 10 of 14	ENST00000358869.5	NP_612398.2	Q8IWE2-1A1MMZ0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FAM114A1	ENST00000358869.5 link	c.1161+143A>C	intron_variant	Intron 10 of 14	1	NM_138389.4	ENSP00000351740.2	Q8IWE2-1
FAM114A1	ENST00000508737.1 link	n.235+143A>C	intron_variant	Intron 1 of 5	1
FAM114A1	ENST00000515037.5 link	c.540+143A>C	intron_variant	Intron 8 of 12	2		ENSP00000424115.1	Q8IWE2-2
FAM114A1	ENST00000512889.1 link	n.*193A>C	downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37274

AN:

152092

Hom.:

5036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.254

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.551

Gnomad SAS

AF:

0.426

Gnomad FIN

AF:

0.0992

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.254

GnomAD4 exome

AF:

0.249

AC:

121597

AN:

489008

Hom.:

18475

AF XY:

0.257

AC XY:

66133

AN XY:

257760

show subpopulations

African (AFR)

AF:

0.236

AC:

3086

AN:

13060

American (AMR)

AF:

0.298

AC:

5818

AN:

19548

Ashkenazi Jewish (ASJ)

AF:

0.332

AC:

4602

AN:

13858

East Asian (EAS)

AF:

0.552

AC:

16499

AN:

29866

South Asian (SAS)

AF:

0.413

AC:

18962

AN:

45864

European-Finnish (FIN)

AF:

0.110

AC:

3171

AN:

28912

Middle Eastern (MID)

AF:

0.307

AC:

945

AN:

3078

European-Non Finnish (NFE)

AF:

0.200

AC:

61592

AN:

308182

Other (OTH)

AF:

0.260

AC:

6922

AN:

26640

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

3886

7772

11657

15543

19429

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

784

1568

2352

3136

3920

<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:

0.245

AC:

37283

AN:

152210

Hom.:

5044

Cov.:

AF XY:

0.246

AC XY:

18287

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.249

AC:

10324

AN:

41528

American (AMR)

AF:

0.305

AC:

4665

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

1208

AN:

3468

East Asian (EAS)

AF:

0.550

AC:

2846

AN:

5170

South Asian (SAS)

AF:

0.426

AC:

2058

AN:

4828

European-Finnish (FIN)

AF:

0.0992

AC:

1053

AN:

10610

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.210

AC:

14284

AN:

68016

Other (OTH)

AF:

0.252

AC:

531

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1395

2790

4186

5581

6976

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.234

Hom.:

19936

Bravo

AF:

0.259

Asia WGS

AF:

0.451

AC:

1571

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.064

(source)

DANN

Benign

0.33

PhyloP100

-1.7

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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