Genetic Variant ARID3C:p.Pro24Pro (chr9-34627943-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001017363.4(ARID3C):c.72G>A(p.Pro24Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 1,551,502 control chromosomes in the GnomAD database, including 91,190 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 0.28 ( 6821 hom., cov: 33)

Exomes 𝑓: 0.34 ( 84369 hom. )

Consequence

ARID3C
NM_001017363.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00300

Variant links:

Genes affected

ARID3C (HGNC:21209): (AT-rich interaction domain 3C) This gene is a member of the ARID (AT-rich interaction domain) family of proteins. The ARID domain is a helix-turn-helix motif-based DNA-binding domain. ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]

ARID3C links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP7

Synonymous conserved (PhyloP=0.003 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID3C	NM_001017363.4 link	c.72G>A	p.Pro24Pro	synonymous_variant	Exon 2 of 8	ENST00000378909.4	NP_001017363.1	A6NKF2
ARID3C	NM_001371945.2 link	c.72G>A	p.Pro24Pro	synonymous_variant	Exon 2 of 7		NP_001358874.1
ARID3C	XM_047422781.1 link	c.522G>A	p.Pro174Pro	synonymous_variant	Exon 3 of 9		XP_047278737.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARID3C	ENST00000378909.4 link	c.72G>A	p.Pro24Pro	synonymous_variant	Exon 2 of 8	2	NM_001017363.4	ENSP00000368189.2		A6NKF2
ARID3C	ENST00000692051.1 link	c.72G>A	p.Pro24Pro	synonymous_variant	Exon 2 of 6			ENSP00000510553.1		A0A8I5QL24

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42190

AN:

152064

Hom.:

6818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.0555

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.312

GnomAD2 exomes

AF:

0.279

AC:

42582

AN:

152848

AF XY:

0.277

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.253

Gnomad ASJ exome

AF:

0.415

Gnomad EAS exome

AF:

0.0545

Gnomad FIN exome

AF:

0.284

Gnomad NFE exome

AF:

0.373

Gnomad OTH exome

AF:

0.337

GnomAD4 exome

AF:

0.337

AC:

471554

AN:

1399320

Hom.:

84369

Cov.:

AF XY:

0.333

AC XY:

230092

AN XY:

690302

show subpopulations

Gnomad4 AFR exome

AF:

0.148

AC:

4672

AN:

31600

Gnomad4 AMR exome

AF:

0.264

AC:

9432

AN:

35726

Gnomad4 ASJ exome

AF:

0.418

AC:

10511

AN:

25126

Gnomad4 EAS exome

AF:

0.0490

AC:

1759

AN:

35884

Gnomad4 SAS exome

AF:

0.163

AC:

12987

AN:

79632

Gnomad4 FIN exome

AF:

0.290

AC:

14183

AN:

48878

Gnomad4 NFE exome

AF:

0.368

AC:

397145

AN:

1078854

Gnomad4 Remaining exome

AF:

0.322

AC:

18632

AN:

57940

Heterozygous variant carriers

18568

37137

55705

74274

92842

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

12478

24956

37434

49912

62390

<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:

0.277

AC:

42208

AN:

152182

Hom.:

6821

Cov.:

AF XY:

0.270

AC XY:

20083

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.151

AC:

0.150942

AN:

0.150942

Gnomad4 AMR

AF:

0.292

AC:

0.291776

AN:

0.291776

Gnomad4 ASJ

AF:

0.420

AC:

0.419931

AN:

0.419931

Gnomad4 EAS

AF:

0.0554

AC:

0.0554482

AN:

0.0554482

Gnomad4 SAS

AF:

0.155

AC:

0.154515

AN:

0.154515

Gnomad4 FIN

AF:

0.276

AC:

0.275537

AN:

0.275537

Gnomad4 NFE

AF:

0.369

AC:

0.369113

AN:

0.369113

Gnomad4 OTH

AF:

0.308

AC:

0.30842

AN:

0.30842

Heterozygous variant carriers

1535

3070

4606

6141

7676

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.350

Hom.:

3167

Bravo

AF:

0.278

Asia WGS

AF:

0.127

AC:

443

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.94

DANN

Benign

0.38

Mutation Taster

=100/0

polymorphism (auto)

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over