Genetic Variant FAM234A:c.1448-30G>T (chr16-264781-G-T) – 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.1448-30G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00517 in 1,606,278 control chromosomes in the GnomAD database, including 400 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 0.028 ( 203 hom., cov: 33)

Exomes 𝑓: 0.0028 ( 197 hom. )

Consequence

FAM234A
NM_032039.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21

Publications

10 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:

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0941 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	UniProt
FAM234A	NM_032039.4	MANE Select	c.1448-30G>T	intron	N/A	NP_114428.1	Q9H0X4-1
FAM234A	NM_001284497.2		c.1448-30G>T	intron	N/A	NP_001271426.1	Q9H0X4-1
FAM234A	NR_104317.2		n.1623+65G>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM234A	ENST00000399932.8	TSL:1 MANE Select	c.1448-30G>T	intron	N/A	ENSP00000382814.3	Q9H0X4-1
FAM234A	ENST00000301678.7	TSL:1	c.1448-30G>T	intron	N/A	ENSP00000301678.3	Q9H0X4-1
FAM234A	ENST00000970193.1		c.1613-30G>T	intron	N/A	ENSP00000640252.1

Frequencies

GnomAD3 genomes

AF:

0.0275

AC:

4187

AN:

152090

Hom.:

203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0967

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00864

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000265

Gnomad OTH

AF:

0.0115

GnomAD2 exomes

AF:

0.00650

AC:

1549

AN:

238412

AF XY:

0.00516

show subpopulations

Gnomad AFR exome

AF:

0.0974

Gnomad AMR exome

AF:

0.00252

Gnomad ASJ exome

AF:

0.00102

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000166

Gnomad OTH exome

AF:

0.00154

GnomAD4 exome

AF:

0.00282

AC:

4101

AN:

1454070

Hom.:

197

Cov.:

AF XY:

0.00243

AC XY:

1756

AN XY:

723414

show subpopulations

African (AFR)

AF:

0.105

AC:

3513

AN:

33392

American (AMR)

AF:

0.00317

AC:

141

AN:

44524

Ashkenazi Jewish (ASJ)

AF:

0.000769

AC:

AN:

26016

East Asian (EAS)

AF:

0.00

AC:

AN:

39546

South Asian (SAS)

AF:

0.000233

AC:

AN:

85996

European-Finnish (FIN)

AF:

0.00

AC:

AN:

48444

Middle Eastern (MID)

AF:

0.00313

AC:

AN:

5746

European-Non Finnish (NFE)

AF:

0.0000585

AC:

AN:

1110190

Other (OTH)

AF:

0.00538

AC:

324

AN:

60216

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

209

418

627

836

1045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

240

360

480

600

<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:

0.0276

AC:

4197

AN:

152208

Hom.:

203

Cov.:

AF XY:

0.0270

AC XY:

2006

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.0966

AC:

4012

AN:

41518

American (AMR)

AF:

0.00863

AC:

132

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.00144

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5172

South Asian (SAS)

AF:

0.000622

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000265

AC:

AN:

67996

Other (OTH)

AF:

0.0114

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

205

411

616

822

1027

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

176

220

<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:

0.0101

Hom.:

Bravo

AF:

0.0312

Asia WGS

AF:

0.00549

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.25

(source)

DANN

Benign

0.59

PhyloP100

-1.2

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