Variant 9-38577242-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_147195.4(ANKRD18A):c.2552A>G(p.Gln851Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 1,532,582 control chromosomes in the GnomAD database, including 3,972 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.059 ( 277 hom., cov: 32)

Exomes 𝑓: 0.070 ( 3695 hom. )

Consequence

ANKRD18A
NM_147195.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0210

Variant links:

Genes affected

ANKRD18A (HGNC:23643): (ankyrin repeat domain 18A)

ANKRD18A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024524033).

BP6

Variant 9-38577242-T-C is Benign according to our data. Variant chr9-38577242-T-C is described in ClinVar as [Benign]. Clinvar id is 769354.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD18A	NM_147195.4 linkuse as main transcript	c.2552A>G	p.Gln851Arg	missense_variant	14/16	ENST00000399703.6	NP_671728.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD18A	ENST00000399703.6 linkuse as main transcript	c.2552A>G	p.Gln851Arg	missense_variant	14/16	1	NM_147195.4	ENSP00000382610	A2	Q8IVF6-1

Frequencies

GnomAD3 genomes

AF:

0.0592

AC:

9010

AN:

152130

Hom.:

276

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0475

Gnomad AMI

AF:

0.0462

Gnomad AMR

AF:

0.0410

Gnomad ASJ

AF:

0.0838

Gnomad EAS

AF:

0.00808

Gnomad SAS

AF:

0.0284

Gnomad FIN

AF:

0.0608

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0753

Gnomad OTH

AF:

0.0573

GnomAD3 exomes

AF:

0.0567

AC:

7729

AN:

136296

Hom.:

281

AF XY:

0.0552

AC XY:

3981

AN XY:

72140

show subpopulations

Gnomad AFR exome

AF:

0.0517

Gnomad AMR exome

AF:

0.0381

Gnomad ASJ exome

AF:

0.0793

Gnomad EAS exome

AF:

0.00705

Gnomad SAS exome

AF:

0.0267

Gnomad FIN exome

AF:

0.0657

Gnomad NFE exome

AF:

0.0753

Gnomad OTH exome

AF:

0.0737

GnomAD4 exome

AF:

0.0703

AC:

97017

AN:

1380334

Hom.:

3695

Cov.:

AF XY:

0.0691

AC XY:

46967

AN XY:

680050

show subpopulations

Gnomad4 AFR exome

AF:

0.0492

Gnomad4 AMR exome

AF:

0.0384

Gnomad4 ASJ exome

AF:

0.0765

Gnomad4 EAS exome

AF:

0.00650

Gnomad4 SAS exome

AF:

0.0265

Gnomad4 FIN exome

AF:

0.0671

Gnomad4 NFE exome

AF:

0.0772

Gnomad4 OTH exome

AF:

0.0669

GnomAD4 genome

AF:

0.0593

AC:

9021

AN:

152248

Hom.:

277

Cov.:

AF XY:

0.0575

AC XY:

4280

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0475

Gnomad4 AMR

AF:

0.0409

Gnomad4 ASJ

AF:

0.0838

Gnomad4 EAS

AF:

0.00810

Gnomad4 SAS

AF:

0.0280

Gnomad4 FIN

AF:

0.0608

Gnomad4 NFE

AF:

0.0753

Gnomad4 OTH

AF:

0.0614

Alfa

AF:

0.0748

Hom.:

137

Bravo

AF:

0.0592

ExAC

AF:

0.0455

AC:

1050

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.51

DEOGEN2

Benign

0.0040

.;T

Eigen

Benign

-0.25

Eigen_PC

Benign

-0.49

FATHMM_MKL

Benign

0.065

LIST_S2

Benign

0.36

T;T

MetaRNN

Benign

0.0025

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.9

.;L

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.53

PROVEAN

Benign

-1.3

.;N

REVEL

Benign

0.070

Sift

Benign

0.24

.;T

Sift4G

Benign

0.20

T;D

Polyphen

0.98

.;D

Vest4

0.0030

MPC

0.035

ClinPred

0.0079

GERP RS

1.5

Varity_R

0.082

gMVP

0.019

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over