Genetic Variant FAM149A:n.926A>G (chr4-186157893-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 ENST00000513030.5(FAM149A):n.926A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.688 in 1,534,524 control chromosomes in the GnomAD database, including 366,389 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 0.65 ( 32362 hom., cov: 34)

Exomes 𝑓: 0.69 ( 334027 hom. )

Consequence

FAM149A
ENST00000513030.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.37

Publications

8 publications found

Variant links:

Genes affected

FAM149A (HGNC:24527): (family with sequence similarity 149 member A)

FAM149A links:

RPSAP70 (HGNC:51923): (ribosomal protein SA pseudogene 70)

RPSAP70 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=-0.63).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
RPSAP70		n.186157893A>G	intragenic_variant
FAM149A	NM_001395294.1 link	c.1602+174A>G	intron_variant	Intron 8 of 13	NP_001382223.1
FAM149A	NM_001367768.3 link	c.1575+174A>G	intron_variant	Intron 8 of 13	NP_001354697.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM149A	ENST00000706927.1 link	c.1602+174A>G		intron_variant	Intron 8 of 13			ENSP00000516649.1		A5PLN7-3

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98543

AN:

152018

Hom.:

32342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.571

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.597

Gnomad EAS

AF:

0.565

Gnomad SAS

AF:

0.660

Gnomad FIN

AF:

0.656

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.709

Gnomad OTH

AF:

0.632

GnomAD2 exomes

AF:

0.629

AC:

88317

AN:

140410

AF XY:

0.638

show subpopulations

Gnomad AFR exome

AF:

0.595

Gnomad AMR exome

AF:

0.456

Gnomad ASJ exome

AF:

0.597

Gnomad EAS exome

AF:

0.579

Gnomad FIN exome

AF:

0.659

Gnomad NFE exome

AF:

0.710

Gnomad OTH exome

AF:

0.638

GnomAD4 exome

AF:

0.693

AC:

957371

AN:

1382388

Hom.:

334027

Cov.:

AF XY:

0.691

AC XY:

471628

AN XY:

682428

show subpopulations

African (AFR)

AF:

0.594

AC:

18761

AN:

31558

American (AMR)

AF:

0.467

AC:

16675

AN:

35738

Ashkenazi Jewish (ASJ)

AF:

0.596

AC:

14975

AN:

25128

East Asian (EAS)

AF:

0.537

AC:

19175

AN:

35732

South Asian (SAS)

AF:

0.647

AC:

50876

AN:

78574

European-Finnish (FIN)

AF:

0.662

AC:

22740

AN:

34340

Middle Eastern (MID)

AF:

0.618

AC:

3515

AN:

5684

European-Non Finnish (NFE)

AF:

0.716

AC:

771945

AN:

1077784

Other (OTH)

AF:

0.669

AC:

38709

AN:

57850

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

13670

27340

41009

54679

68349

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19464

38928

58392

77856

97320

<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:

0.648

AC:

98608

AN:

152136

Hom.:

32362

Cov.:

AF XY:

0.642

AC XY:

47739

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.600

AC:

24878

AN:

41488

American (AMR)

AF:

0.549

AC:

8402

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.597

AC:

2073

AN:

3470

East Asian (EAS)

AF:

0.565

AC:

2915

AN:

5162

South Asian (SAS)

AF:

0.659

AC:

3176

AN:

4818

European-Finnish (FIN)

AF:

0.656

AC:

6938

AN:

10580

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.709

AC:

48220

AN:

68000

Other (OTH)

AF:

0.629

AC:

1332

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1775

3550

5324

7099

8874

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

804

1608

2412

3216

4020

<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:

0.676

Hom.:

21761

Bravo

AF:

0.634

Asia WGS

AF:

0.625

AC:

2173

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

4.5

(source)

DANN

Benign

0.58

PhyloP100

6.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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