dbSNP rs3091367: ANKRD54:c.*129G>C (chr22-37831814-C-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_138797.4(ANKRD54):c.*129G>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 0.242 in 890,492 control chromosomes in the GnomAD database, including 27,556 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 0.27 ( 5900 hom., cov: 33)

Exomes 𝑓: 0.24 ( 21656 hom. )

Consequence

ANKRD54
NM_138797.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.71

Publications

5 publications found

Variant links:

Genes affected

ANKRD54 (HGNC:25185): (ankyrin repeat domain 54) Predicted to enable protein kinase regulator activity. Predicted to be involved in positive regulation of erythrocyte differentiation; regulation of intracellular signal transduction; and regulation of protein kinase activity. Predicted to act upstream of or within nucleocytoplasmic transport. Predicted to be located in midbody. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD54 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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD54	NM_138797.4 link	c.*129G>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000215941.9	NP_620152.1	Q6NXT1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD54	ENST00000215941.9 link	c.*129G>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_138797.4	ENSP00000215941.4		Q6NXT1-1

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41313

AN:

152034

Hom.:

5901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.351

Gnomad AMI

AF:

0.303

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.0975

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.285

GnomAD4 exome

AF:

0.236

AC:

174555

AN:

738340

Hom.:

21656

Cov.:

AF XY:

0.237

AC XY:

88783

AN XY:

375242

show subpopulations

African (AFR)

AF:

0.359

AC:

6642

AN:

18496

American (AMR)

AF:

0.301

AC:

7497

AN:

24924

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

4151

AN:

16194

East Asian (EAS)

AF:

0.0700

AC:

2262

AN:

32312

South Asian (SAS)

AF:

0.222

AC:

12260

AN:

55304

European-Finnish (FIN)

AF:

0.250

AC:

8032

AN:

32106

Middle Eastern (MID)

AF:

0.313

AC:

1276

AN:

4082

European-Non Finnish (NFE)

AF:

0.238

AC:

123600

AN:

519404

Other (OTH)

AF:

0.249

AC:

8835

AN:

35518

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

6396

12792

19188

25584

31980

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.272

AC:

41342

AN:

152152

Hom.:

5900

Cov.:

AF XY:

0.268

AC XY:

19966

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.350

AC:

14537

AN:

41524

American (AMR)

AF:

0.300

AC:

4592

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

904

AN:

3472

East Asian (EAS)

AF:

0.0975

AC:

505

AN:

5178

South Asian (SAS)

AF:

0.200

AC:

965

AN:

4816

European-Finnish (FIN)

AF:

0.248

AC:

2627

AN:

10572

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.239

AC:

16243

AN:

67984

Other (OTH)

AF:

0.281

AC:

595

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1583

3167

4750

6334

7917

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.141

Hom.:

248

Bravo

AF:

0.281

Asia WGS

AF:

0.166

AC:

581

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.6

(source)

DANN

Benign

0.55

PhyloP100

1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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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rs3091367

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