Genetic Variant ENSG00000230074:n.86+20000C>A (chr9-34723038-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000664167.1(ENSG00000230074):n.86+20000C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 708,848 control chromosomes in the GnomAD database, including 25,119 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 0.21 ( 4275 hom., cov: 32)

Exomes 𝑓: 0.26 ( 20844 hom. )

Consequence

ENSG00000230074
ENST00000664167.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.14

Publications

13 publications found

Variant links:

Genes affected

ENSG00000230074 (HGNC:):

ENSG00000230074 links:

PHF24 (HGNC:29180): (PHD finger protein 24) Predicted to enable metal ion binding activity. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. [provided by Alliance of Genome Resources, Apr 2022]

PHF24 links:

SPATA31F1 (HGNC:41911): (SPATA31 subfamily F member 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SPATA31F1 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
PHF24	XM_047423102.1 link	c.133+20000C>A	intron_variant	Intron 4 of 11		XP_047279058.1
PHF24	XM_047423103.1 link	c.70+20000C>A	intron_variant	Intron 2 of 9		XP_047279059.1
SPATA31F1	NM_001141917.2 link	c.*194G>T	downstream_gene_variant		ENST00000378788.4	NP_001135389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA31F1	ENST00000378788.4 link	c.*194G>T		downstream_gene_variant		2	NM_001141917.2	ENSP00000417711.1		Q6ZU69

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31593

AN:

152030

Hom.:

4277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0546

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.0529

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.208

GnomAD4 exome

AF:

0.262

AC:

145824

AN:

556700

Hom.:

20844

Cov.:

AF XY:

0.259

AC XY:

73903

AN XY:

285050

show subpopulations

African (AFR)

AF:

0.0509

AC:

758

AN:

14906

American (AMR)

AF:

0.196

AC:

3612

AN:

18400

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

2911

AN:

14272

East Asian (EAS)

AF:

0.0428

AC:

1337

AN:

31266

South Asian (SAS)

AF:

0.201

AC:

8402

AN:

41848

European-Finnish (FIN)

AF:

0.283

AC:

8280

AN:

29302

Middle Eastern (MID)

AF:

0.203

AC:

437

AN:

2152

European-Non Finnish (NFE)

AF:

0.301

AC:

112856

AN:

375068

Other (OTH)

AF:

0.245

AC:

7231

AN:

29486

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

4997

9994

14992

19989

24986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1784

3568

5352

7136

8920

<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:

0.208

AC:

31589

AN:

152148

Hom.:

4275

Cov.:

AF XY:

0.205

AC XY:

15240

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0544

AC:

2260

AN:

41534

American (AMR)

AF:

0.205

AC:

3133

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

682

AN:

3466

East Asian (EAS)

AF:

0.0535

AC:

277

AN:

5182

South Asian (SAS)

AF:

0.195

AC:

942

AN:

4822

European-Finnish (FIN)

AF:

0.267

AC:

2821

AN:

10556

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.304

AC:

20690

AN:

67986

Other (OTH)

AF:

0.206

AC:

435

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1158

2315

3473

4630

5788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

350

700

1050

1400

1750

<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:

0.269

Hom.:

9910

Bravo

AF:

0.196

Asia WGS

AF:

0.108

AC:

374

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.13

(source)

DANN

Benign

0.31

PhyloP100

-3.1

Mutation Taster

=98/2

polymorphism

(source)

Splicing

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