Variant 11-94498091-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000544612.6(ANKRD49):c.279C>G(p.Leu93=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 1,609,474 control chromosomes in the GnomAD database, including 252,940 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 25048 hom., cov: 31)

Exomes 𝑓: 0.56 ( 227892 hom. )

Consequence

ANKRD49
ENST00000544612.6 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.25

Variant links:

Genes affected

ANKRD49 (HGNC:25970): (ankyrin repeat domain 49) Involved in positive regulation of transcription, DNA-templated. Predicted to be located in nucleus. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD49 links:

MRE11 (HGNC:):

MRE11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 11-94498091-C-G is Benign according to our data. Variant chr11-94498091-C-G is described in ClinVar as [Benign]. Clinvar id is 403103.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ANKRD49	NM_017704.3 linkuse as main transcript	c.279C>G	p.Leu93=	synonymous_variant	3/3	ENST00000544612.6	NP_060174.2
ANKRD49	XM_017017941.2 linkuse as main transcript	c.279C>G	p.Leu93=	synonymous_variant	3/3		XP_016873430.1
MRE11	XM_011542837.3 linkuse as main transcript	c.-105-5185G>C		intron_variant			XP_011541139.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD49	ENST00000544612.6 linkuse as main transcript	c.279C>G	p.Leu93=	synonymous_variant	3/3	1	NM_017704.3	ENSP00000440396	P1

Frequencies

GnomAD3 genomes

AF:

0.572

AC:

86744

AN:

151774

Hom.:

25026

Cov.:

show subpopulations

Gnomad AFR

AF:

0.630

Gnomad AMI

AF:

0.774

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.586

Gnomad EAS

AF:

0.520

Gnomad SAS

AF:

0.435

Gnomad FIN

AF:

0.535

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.553

GnomAD3 exomes

AF:

0.533

AC:

132508

AN:

248708

Hom.:

35769

AF XY:

0.530

AC XY:

71214

AN XY:

134440

show subpopulations

Gnomad AFR exome

AF:

0.627

Gnomad AMR exome

AF:

0.460

Gnomad ASJ exome

AF:

0.560

Gnomad EAS exome

AF:

0.520

Gnomad SAS exome

AF:

0.433

Gnomad FIN exome

AF:

0.540

Gnomad NFE exome

AF:

0.566

Gnomad OTH exome

AF:

0.540

GnomAD4 exome

AF:

0.557

AC:

811808

AN:

1457582

Hom.:

227892

Cov.:

AF XY:

0.553

AC XY:

400514

AN XY:

724704

show subpopulations

Gnomad4 AFR exome

AF:

0.626

Gnomad4 AMR exome

AF:

0.467

Gnomad4 ASJ exome

AF:

0.563

Gnomad4 EAS exome

AF:

0.484

Gnomad4 SAS exome

AF:

0.431

Gnomad4 FIN exome

AF:

0.542

Gnomad4 NFE exome

AF:

0.572

Gnomad4 OTH exome

AF:

0.558

GnomAD4 genome

AF:

0.572

AC:

86817

AN:

151892

Hom.:

25048

Cov.:

AF XY:

0.565

AC XY:

41962

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.630

Gnomad4 AMR

AF:

0.498

Gnomad4 ASJ

AF:

0.586

Gnomad4 EAS

AF:

0.521

Gnomad4 SAS

AF:

0.434

Gnomad4 FIN

AF:

0.535

Gnomad4 NFE

AF:

0.569

Gnomad4 OTH

AF:

0.559

Alfa

AF:

0.534

Hom.:

5607

Bravo

AF:

0.575

Asia WGS

AF:

0.500

AC:

1739

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.44

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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