dbSNP rs2296136: ANKRD16:p.Ala128Gly (chr10-5887999-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019046.3(ANKRD16):c.383C>G(p.Ala128Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 1,614,122 control chromosomes in the GnomAD database, including 1,783 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.035 ( 165 hom., cov: 32)

Exomes 𝑓: 0.041 ( 1618 hom. )

Consequence

ANKRD16
NM_019046.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.65

Variant links:

Genes affected

ANKRD16 (HGNC:23471): (ankyrin repeat domain 16) Predicted to be involved in tRNA modification. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD16 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0026624203).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD16	NM_019046.3 link	c.383C>G	p.Ala128Gly	missense_variant	Exon 2 of 8	ENST00000380094.10	NP_061919.1	Q6P6B7-1
ANKRD16	NM_001009941.3 link	c.383C>G	p.Ala128Gly	missense_variant	Exon 2 of 7		NP_001009941.1	Q6P6B7-1
ANKRD16	NM_001009943.3 link	c.383C>G	p.Ala128Gly	missense_variant	Exon 2 of 6		NP_001009943.1	Q6P6B7-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ANKRD16	ENST00000380094.10 link	c.383C>G	p.Ala128Gly	missense_variant	Exon 2 of 8	2	NM_019046.3	ENSP00000369436.4	Q6P6B7-1
ANKRD16	ENST00000380092.8 link	c.383C>G	p.Ala128Gly	missense_variant	Exon 2 of 7	1		ENSP00000369434.4	Q6P6B7-1
ANKRD16	ENST00000191063.8 link	c.383C>G	p.Ala128Gly	missense_variant	Exon 2 of 6	3		ENSP00000352361.6	Q6P6B7-2
ANKRD16	ENST00000492368.1 link	n.-29C>G		upstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0346

AC:

5272

AN:

152176

Hom.:

164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00794

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.0293

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.0877

Gnomad FIN

AF:

0.0751

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0360

Gnomad OTH

AF:

0.0325

GnomAD3 exomes

AF:

0.0527

AC:

13264

AN:

251492

Hom.:

544

AF XY:

0.0538

AC XY:

7307

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.00707

Gnomad AMR exome

AF:

0.0539

Gnomad ASJ exome

AF:

0.0118

Gnomad EAS exome

AF:

0.143

Gnomad SAS exome

AF:

0.0830

Gnomad FIN exome

AF:

0.0690

Gnomad NFE exome

AF:

0.0369

Gnomad OTH exome

AF:

0.0482

GnomAD4 exome

AF:

0.0408

AC:

59581

AN:

1461828

Hom.:

1618

Cov.:

AF XY:

0.0418

AC XY:

30375

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.00597

Gnomad4 AMR exome

AF:

0.0498

Gnomad4 ASJ exome

AF:

0.0129

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.0819

Gnomad4 FIN exome

AF:

0.0682

Gnomad4 NFE exome

AF:

0.0353

Gnomad4 OTH exome

AF:

0.0409

GnomAD4 genome

AF:

0.0347

AC:

5280

AN:

152294

Hom.:

165

Cov.:

AF XY:

0.0380

AC XY:

2832

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.00791

Gnomad4 AMR

AF:

0.0294

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.134

Gnomad4 SAS

AF:

0.0871

Gnomad4 FIN

AF:

0.0751

Gnomad4 NFE

AF:

0.0360

Gnomad4 OTH

AF:

0.0365

Alfa

AF:

0.0315

Hom.:

Bravo

AF:

0.0296

TwinsUK

AF:

0.0359

AC:

133

ALSPAC

AF:

0.0355

AC:

137

ESP6500AA

AF:

0.00999

AC:

ESP6500EA

AF:

0.0349

AC:

300

ExAC

AF:

0.0529

AC:

6417

Asia WGS

AF:

0.130

AC:

449

AN:

3478

EpiCase

AF:

0.0303

EpiControl

AF:

0.0312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Uncertain

-0.080

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.022

T;T;.

Eigen

Uncertain

0.45

Eigen_PC

Uncertain

0.31

FATHMM_MKL

Uncertain

0.94

LIST_S2

Uncertain

0.88

.;D;D

MetaRNN

Benign

0.0027

T;T;T

MetaSVM

Benign

-0.85

MutationAssessor

Uncertain

2.7

M;M;M

PrimateAI

Benign

0.46

PROVEAN

Uncertain

-3.8

D;D;D

REVEL

Uncertain

0.33

Sift

Uncertain

0.011

D;D;D

Sift4G

Pathogenic

0.0

D;D;D

Polyphen

1.0

D;D;.

Vest4

0.28

MPC

0.75

ClinPred

0.021

GERP RS

2.9

Varity_R

0.51

gMVP

0.57

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