Variant 2-95853727-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001393982.1(ANKRD36C):c.6153A>G(p.Leu2051Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,588,308 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 30)

Exomes 𝑓: 0.0012 ( 1 hom. )

Consequence

ANKRD36C
NM_001393982.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.845

Variant links:

Genes affected

ANKRD36C (HGNC:32946): (ankyrin repeat domain 36C)

ANKRD36C links:

ANKRD36C (HGNC:):

ANKRD36C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 2-95853727-T-C is Benign according to our data. Variant chr2-95853727-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2651122.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.845 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD36C	NM_001393982.1 linkuse as main transcript	c.6153A>G	p.Leu2051Leu	synonymous_variant	84/88	ENST00000295246.7	NP_001380911.1
ANKRD36C	NM_001310154.3 linkuse as main transcript	c.6228A>G	p.Leu2076Leu	synonymous_variant	85/89		NP_001297083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ANKRD36C	ENST00000295246.7 linkuse as main transcript	c.6153A>G	p.Leu2051Leu	synonymous_variant	84/88	5	NM_001393982.1	ENSP00000295246.7	A0A8J8YUB5
ANKRD36C	ENST00000612359.4 linkuse as main transcript	c.207A>G	p.Leu69Leu	synonymous_variant	2/6	1		ENSP00000485004.1	A0A0C4DH05
ANKRD36C	ENST00000488721.5 linkuse as main transcript	n.1303A>G		non_coding_transcript_exon_variant	4/4	1
ANKRD36C	ENST00000456556.5 linkuse as main transcript	c.5130A>G	p.Leu1710Leu	synonymous_variant	64/67	5		ENSP00000403302.1	Q5JPF3-1

Frequencies

GnomAD3 genomes

AF:

0.00101

AC:

154

AN:

152080

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000290

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000656

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00188

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.000808

AC:

143

AN:

176890

Hom.:

AF XY:

0.000764

AC XY:

AN XY:

92940

show subpopulations

Gnomad AFR exome

AF:

0.000270

Gnomad AMR exome

AF:

0.000648

Gnomad ASJ exome

AF:

0.000225

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000169

Gnomad FIN exome

AF:

0.0000567

Gnomad NFE exome

AF:

0.00160

Gnomad OTH exome

AF:

0.000419

GnomAD4 exome

AF:

0.00124

AC:

1780

AN:

1436110

Hom.:

Cov.:

AF XY:

0.00125

AC XY:

888

AN XY:

711942

show subpopulations

Gnomad4 AFR exome

AF:

0.0000906

Gnomad4 AMR exome

AF:

0.000578

Gnomad4 ASJ exome

AF:

0.0000777

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000217

Gnomad4 FIN exome

AF:

0.0000577

Gnomad4 NFE exome

AF:

0.00152

Gnomad4 OTH exome

AF:

0.00101

GnomAD4 genome

AF:

0.00101

AC:

154

AN:

152198

Hom.:

Cov.:

AF XY:

0.00102

AC XY:

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.000289

Gnomad4 AMR

AF:

0.000655

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00188

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00154

Hom.:

Bravo

AF:

0.00113

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

ANKRD36C: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.86

DANN

Benign

0.36

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