dbSNP rs2276919: FAM149A:c.1602+174A>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 NM_001395294.1(FAM149A):c.1602+174A>G variant causes a intron 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
NM_001395294.1 intron

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395294.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM149A	NM_001395294.1	MANE Select	c.1602+174A>G	intron	N/A	NP_001382223.1	A5PLN7-3
FAM149A	NM_001367768.3		c.1575+174A>G	intron	N/A	NP_001354697.1	A0A0A0MRZ3
FAM149A	NM_001006655.3		c.729+174A>G	intron	N/A	NP_001006656.1	A5PLN7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM149A	ENST00000706927.1	MANE Select	c.1602+174A>G	intron	N/A	ENSP00000516649.1	A5PLN7-3
FAM149A	ENST00000227065.8	TSL:1	c.729+174A>G	intron	N/A	ENSP00000227065.4	A5PLN7-2
FAM149A	ENST00000513030.5	TSL:1	n.926A>G	non_coding_transcript_exon	Exon 7 of 7

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over