Genetic Variant ARHGEF26-AS1:n.357+37976C>T (chr3-154070693-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 ENST00000491862.6(ARHGEF26-AS1):n.357+37976C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 152,134 control chromosomes in the GnomAD database, including 385 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 0.046 ( 385 hom., cov: 32)

Consequence

ARHGEF26-AS1
ENST00000491862.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.689

Publications

0 publications found

Variant links:

Genes affected

ARHGEF26-AS1 (HGNC:41048): (ARHGEF26 antisense RNA 1)

ARHGEF26-AS1 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGEF26-AS1	NR_037901.1 link	n.256+37976C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ARHGEF26-AS1	ENST00000491862.6 link	n.357+37976C>T	intron_variant	Intron 2 of 3	1
ARHGEF26-AS1	ENST00000467912.6 link	n.360-40314C>T	intron_variant	Intron 2 of 3	3
ARHGEF26-AS1	ENST00000479270.6 link	n.378+37976C>T	intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.0463

AC:

7031

AN:

152016

Hom.:

383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0255

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.00560

Gnomad FIN

AF:

0.00302

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00816

Gnomad OTH

AF:

0.0368

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0464

AC:

7061

AN:

152134

Hom.:

385

Cov.:

AF XY:

0.0451

AC XY:

3355

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.130

AC:

5383

AN:

41482

American (AMR)

AF:

0.0255

AC:

390

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.00548

AC:

AN:

3466

East Asian (EAS)

AF:

0.111

AC:

577

AN:

5186

South Asian (SAS)

AF:

0.00560

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00302

AC:

AN:

10598

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00816

AC:

555

AN:

67994

Other (OTH)

AF:

0.0369

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

318

635

953

1270

1588

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<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:

0.0307

Hom.:

Bravo

AF:

0.0519

Asia WGS

AF:

0.0720

AC:

251

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.11

(source)

DANN

Benign

0.50

PhyloP100

-0.69

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over