Genetic Variant ARHGAP27:c.*315T>C (chr17-45395141-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_001282290.2(ARHGAP27):c.*315T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 413,192 control chromosomes in the GnomAD database, including 15,069 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 0.23 ( 4464 hom., cov: 32)

Exomes 𝑓: 0.27 ( 10605 hom. )

Consequence

ARHGAP27
NM_001282290.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.237

Publications

13 publications found

Variant links:

Genes affected

ARHGAP27 (HGNC:31813): (Rho GTPase activating protein 27) This gene encodes a member of a large family of proteins that activate Rho-type guanosine triphosphate (GTP) metabolizing enzymes. The encoded protein may pay a role in clathrin-mediated endocytosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2013]

ARHGAP27 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282290.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ARHGAP27	NM_001282290.2	MANE Select	c.*315T>C	3_prime_UTR	Exon 20 of 20	NP_001269219.1
ARHGAP27	NR_169600.1		n.3156T>C	non_coding_transcript_exon	Exon 18 of 18
ARHGAP27	NR_169601.1		n.3542T>C	non_coding_transcript_exon	Exon 21 of 21

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ARHGAP27	ENST00000685559.1	MANE Select	c.*315T>C	3_prime_UTR	Exon 20 of 20	ENSP00000509127.1
ARHGAP27	ENST00000528384.5	TSL:1	c.*315T>C	3_prime_UTR	Exon 15 of 15	ENSP00000431591.1
ARHGAP27	ENST00000531735.5	TSL:5	n.3522T>C	non_coding_transcript_exon	Exon 17 of 17

Frequencies

GnomAD3 genomes

AF:

0.227

AC:

34520

AN:

151894

Hom.:

4466

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0953

Gnomad AMI

AF:

0.237

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.308

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.325

Gnomad NFE

AF:

0.273

Gnomad OTH

AF:

0.237

GnomAD4 exome

AF:

0.275

AC:

71716

AN:

261180

Hom.:

10605

Cov.:

AF XY:

0.276

AC XY:

37602

AN XY:

136126

show subpopulations

African (AFR)

AF:

0.0947

AC:

684

AN:

7220

American (AMR)

AF:

0.201

AC:

1670

AN:

8324

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

2097

AN:

8386

East Asian (EAS)

AF:

0.377

AC:

6198

AN:

16440

South Asian (SAS)

AF:

0.289

AC:

7395

AN:

25572

European-Finnish (FIN)

AF:

0.353

AC:

5929

AN:

16812

Middle Eastern (MID)

AF:

0.306

AC:

375

AN:

1224

European-Non Finnish (NFE)

AF:

0.268

AC:

43171

AN:

161308

Other (OTH)

AF:

0.264

AC:

4197

AN:

15894

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2399

4798

7197

9596

11995

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.227

AC:

34531

AN:

152012

Hom.:

4464

Cov.:

AF XY:

0.234

AC XY:

17348

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.0956

AC:

3967

AN:

41480

American (AMR)

AF:

0.216

AC:

3305

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

854

AN:

3462

East Asian (EAS)

AF:

0.351

AC:

1808

AN:

5146

South Asian (SAS)

AF:

0.307

AC:

1481

AN:

4822

European-Finnish (FIN)

AF:

0.354

AC:

3739

AN:

10564

Middle Eastern (MID)

AF:

0.332

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.273

AC:

18564

AN:

67942

Other (OTH)

AF:

0.237

AC:

500

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1336

2672

4009

5345

6681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

376

752

1128

1504

1880

<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:

0.258

Hom.:

18465

Bravo

AF:

0.211

Asia WGS

AF:

0.267

AC:

930

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.3

(source)

DANN

Benign

0.29

PhyloP100

0.24

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