Variant 10-5878158-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_019046.3(ANKRD16):c.1058A>G(p.Gln353Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 1,613,964 control chromosomes in the GnomAD database, including 599,274 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict 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 same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.83 ( 52316 hom., cov: 33)

Exomes 𝑓: 0.86 ( 546958 hom. )

Consequence

ANKRD16
NM_019046.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0590

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=9.275913E-7).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ANKRD16	NM_019046.3 linkuse as main transcript	c.1058A>G	p.Gln353Arg	missense_variant	7/8	ENST00000380094.10	NP_061919.1
ANKRD16	NM_001009941.3 linkuse as main transcript	c.1058A>G	p.Gln353Arg	missense_variant	7/7		NP_001009941.1
ANKRD16	NM_001009943.3 linkuse as main transcript	c.*64A>G		3_prime_UTR_variant	6/6		NP_001009943.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD16	ENST00000380094.10 linkuse as main transcript	c.1058A>G	p.Gln353Arg	missense_variant	7/8	2	NM_019046.3	ENSP00000369436	P1	Q6P6B7-1
ANKRD16	ENST00000380092.8 linkuse as main transcript	c.1058A>G	p.Gln353Arg	missense_variant	7/7	1		ENSP00000369434	P1	Q6P6B7-1
ANKRD16	ENST00000191063.8 linkuse as main transcript	c.*64A>G		3_prime_UTR_variant	6/6	3		ENSP00000352361		Q6P6B7-2

Frequencies

GnomAD3 genomes

AF:

0.826

AC:

125602

AN:

152068

Hom.:

52276

Cov.:

show subpopulations

Gnomad AFR

AF:

0.717

Gnomad AMI

AF:

0.921

Gnomad AMR

AF:

0.874

Gnomad ASJ

AF:

0.815

Gnomad EAS

AF:

0.855

Gnomad SAS

AF:

0.784

Gnomad FIN

AF:

0.882

Gnomad MID

AF:

0.783

Gnomad NFE

AF:

0.873

Gnomad OTH

AF:

0.825

GnomAD3 exomes

AF:

0.858

AC:

215702

AN:

251260

Hom.:

92968

AF XY:

0.854

AC XY:

115985

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.718

Gnomad AMR exome

AF:

0.924

Gnomad ASJ exome

AF:

0.818

Gnomad EAS exome

AF:

0.859

Gnomad SAS exome

AF:

0.785

Gnomad FIN exome

AF:

0.885

Gnomad NFE exome

AF:

0.877

Gnomad OTH exome

AF:

0.859

GnomAD4 exome

AF:

0.864

AC:

1263251

AN:

1461778

Hom.:

546958

Cov.:

AF XY:

0.862

AC XY:

626607

AN XY:

727188

show subpopulations

Gnomad4 AFR exome

AF:

0.706

Gnomad4 AMR exome

AF:

0.917

Gnomad4 ASJ exome

AF:

0.819

Gnomad4 EAS exome

AF:

0.859

Gnomad4 SAS exome

AF:

0.788

Gnomad4 FIN exome

AF:

0.885

Gnomad4 NFE exome

AF:

0.874

Gnomad4 OTH exome

AF:

0.852

GnomAD4 genome

AF:

0.826

AC:

125700

AN:

152186

Hom.:

52316

Cov.:

AF XY:

0.826

AC XY:

61473

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.717

Gnomad4 AMR

AF:

0.874

Gnomad4 ASJ

AF:

0.815

Gnomad4 EAS

AF:

0.854

Gnomad4 SAS

AF:

0.786

Gnomad4 FIN

AF:

0.882

Gnomad4 NFE

AF:

0.873

Gnomad4 OTH

AF:

0.826

Alfa

AF:

0.865

Hom.:

143790

Bravo

AF:

0.823

TwinsUK

AF:

0.869

AC:

3221

ALSPAC

AF:

0.873

AC:

3364

ESP6500AA

AF:

0.715

AC:

3152

ESP6500EA

AF:

0.876

AC:

7533

ExAC

AF:

0.852

AC:

103481

Asia WGS

AF:

0.842

AC:

2924

AN:

3478

EpiCase

AF:

0.874

EpiControl

AF:

0.873

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.34

DANN

Benign

0.97

DEOGEN2

Benign

0.00046

T;T

Eigen

Benign

-0.56

Eigen_PC

Benign

-0.39

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.29

.;T

MetaRNN

Benign

9.3e-7

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.5

L;L

MutationTaster

Benign

0.53

P;P;P

PrimateAI

Benign

0.23

PROVEAN

Benign

-0.73

N;N

REVEL

Benign

0.051

Sift

Benign

0.38

T;T

Sift4G

Benign

0.48

T;T

Polyphen

0.0010

B;B

Vest4

0.036

MPC

0.20

ClinPred

0.0043

GERP RS

3.8

Varity_R

0.021

gMVP

0.45

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