2-95853778-C-T

Variant summary

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

The NM_001393982.1(ANKRD36C):​c.6102G>A​(p.Ser2034Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 1,604,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000025 ( 0 hom. )

Consequence

ANKRD36C
NM_001393982.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.444
Variant links:
Genes affected
ANKRD36C (HGNC:32946): (ankyrin repeat domain 36C)

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=-0.84).
BP6
Variant 2-95853778-C-T is Benign according to our data. Variant chr2-95853778-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651124.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.444 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ANKRD36CNM_001393982.1 linkuse as main transcriptc.6102G>A p.Ser2034Ser synonymous_variant 84/88 ENST00000295246.7 NP_001380911.1
ANKRD36CNM_001310154.3 linkuse as main transcriptc.6177G>A p.Ser2059Ser synonymous_variant 85/89 NP_001297083.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANKRD36CENST00000295246.7 linkuse as main transcriptc.6102G>A p.Ser2034Ser synonymous_variant 84/885 NM_001393982.1 ENSP00000295246.7 A0A8J8YUB5
ANKRD36CENST00000612359.4 linkuse as main transcriptc.156G>A p.Ser52Ser synonymous_variant 2/61 ENSP00000485004.1 A0A0C4DH05
ANKRD36CENST00000488721.5 linkuse as main transcriptn.1252G>A non_coding_transcript_exon_variant 4/41
ANKRD36CENST00000456556.5 linkuse as main transcriptc.5079G>A p.Ser1693Ser synonymous_variant 64/675 ENSP00000403302.1 Q5JPF3-1

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152140
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000214
AC:
5
AN:
233184
Hom.:
0
AF XY:
0.0000239
AC XY:
3
AN XY:
125324
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000700
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000291
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000248
AC:
36
AN:
1452288
Hom.:
0
Cov.:
30
AF XY:
0.0000236
AC XY:
17
AN XY:
721716
show subpopulations
Gnomad4 AFR exome
AF:
0.0000900
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000506
Gnomad4 SAS exome
AF:
0.0000471
Gnomad4 FIN exome
AF:
0.0000189
Gnomad4 NFE exome
AF:
0.0000235
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152140
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.0000483
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.00000756

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2023ANKRD36C: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.4
DANN
Benign
0.30
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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.

Other links and lift over

dbSNP: rs772303036; hg19: chr2-96519526; COSMIC: COSV69438282; COSMIC: COSV69438282; API