Genetic Variant FAM234A:c.577+221G>A (chr16-260381-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_032039.4(FAM234A):c.577+221G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 593,928 control chromosomes in the GnomAD database, including 386 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 0.033 ( 299 hom., cov: 33)

Exomes 𝑓: 0.0041 ( 87 hom. )

Consequence

FAM234A
NM_032039.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.442

Publications

9 publications found

Variant links:

Genes affected

FAM234A (HGNC:14163): (family with sequence similarity 234 member A) Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

FAM234A links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032039.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FAM234A	NM_032039.4	MANE Select	c.577+221G>A	intron	N/A	NP_114428.1
FAM234A	NM_001284497.2		c.577+221G>A	intron	N/A	NP_001271426.1
FAM234A	NR_104317.2		n.753+221G>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FAM234A	ENST00000399932.8	TSL:1 MANE Select	c.577+221G>A	intron	N/A	ENSP00000382814.3
FAM234A	ENST00000301678.7	TSL:1	c.577+221G>A	intron	N/A	ENSP00000301678.3
FAM234A	ENST00000301679.7	TSL:2	c.577+221G>A	intron	N/A	ENSP00000301679.2

Frequencies

GnomAD3 genomes

AF:

0.0328

AC:

4989

AN:

152206

Hom.:

296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000309

Gnomad OTH

AF:

0.0158

GnomAD2 exomes

AF:

0.0108

AC:

768

AN:

71004

AF XY:

0.00884

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.00321

Gnomad ASJ exome

AF:

0.000464

Gnomad EAS exome

AF:

0.000230

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000279

Gnomad OTH exome

AF:

0.00129

GnomAD4 exome

AF:

0.00407

AC:

1797

AN:

441604

Hom.:

Cov.:

AF XY:

0.00326

AC XY:

759

AN XY:

233078

show subpopulations

African (AFR)

AF:

0.112

AC:

1409

AN:

12582

American (AMR)

AF:

0.00445

AC:

AN:

20890

Ashkenazi Jewish (ASJ)

AF:

0.000887

AC:

AN:

13530

East Asian (EAS)

AF:

0.0000675

AC:

AN:

29634

South Asian (SAS)

AF:

0.000818

AC:

AN:

47670

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29206

Middle Eastern (MID)

AF:

0.00407

AC:

AN:

3438

European-Non Finnish (NFE)

AF:

0.000170

AC:

AN:

259450

Other (OTH)

AF:

0.00730

AC:

184

AN:

25204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

174

261

348

435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.0329

AC:

5009

AN:

152324

Hom.:

299

Cov.:

AF XY:

0.0323

AC XY:

2406

AN XY:

74496

show subpopulations

African (AFR)

AF:

0.115

AC:

4775

AN:

41558

American (AMR)

AF:

0.0107

AC:

164

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00144

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5192

South Asian (SAS)

AF:

0.00145

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000309

AC:

AN:

68028

Other (OTH)

AF:

0.0156

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

230

460

690

920

1150

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.0152

Hom.:

203

Bravo

AF:

0.0371

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.1

(source)

DANN

Benign

0.52

PhyloP100

0.44

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