chr2-95902947-G-A

Position:

• chr2-95902947-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001393982.1(ANKRD36C):​c.3204C>T​(p.Asp1068Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000481 in 1,587,370 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00085 (5 hom., cov: 30)
  • Exomes 𝑓: 0.00044 (13 hom.)
• Consequence: ANKRD36C NM_001393982.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.88

Genes affected

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

ANKRD36C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 2-95902947-G-A is Benign according to our data. Variant chr2-95902947-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651129.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-4.88 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD36C	NM_001393982.1	c.3204C>T	p.Asp1068Asp	synonymous_variant	54/88	ENST00000295246.7	NP_001380911.1
ANKRD36C	NM_001310154.3	c.3279C>T	p.Asp1093Asp	synonymous_variant	55/89		NP_001297083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD36C	ENST00000295246.7	c.3204C>T	p.Asp1068Asp	synonymous_variant	54/88	5	NM_001393982.1	ENSP00000295246.7
ANKRD36C	ENST00000456556.5	c.2654-3611C>T		intron_variant		5		ENSP00000403302.1
ANKRD36C	ENST00000531153.5	n.985C>T		non_coding_transcript_exon_variant	7/31	5
ANKRD36C	ENST00000534304.5	n.*982-3611C>T		intron_variant		5		ENSP00000433685.1

Frequencies

GnomAD3 genomes AF: 0.000847 AC: 127 AN: 149980 Hom.: 5 Cov.: 30

Gnomad AFR AF: 0.00135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000667

Gnomad ASJ AF: 0.00493

Gnomad EAS AF: 0.000985

Gnomad SAS AF: 0.00189

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000461

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000442 AC: 635 AN: 1437278 Hom.: 13 Cov.: 32 AF XY: 0.000454 AC XY: 324 AN XY: 713962

Gnomad4 AFR exome AF: 0.000975

Gnomad4 AMR exome AF: 0.00151

Gnomad4 ASJ exome AF: 0.00433

Gnomad4 EAS exome AF: 0.00146

Gnomad4 SAS exome AF: 0.000867

Gnomad4 FIN exome AF: 0.0000385

Gnomad4 NFE exome AF: 0.000241

Gnomad4 OTH exome AF: 0.000525

GnomAD4 genome AF: 0.000853 AC: 128 AN: 150092 Hom.: 5 Cov.: 30 AF XY: 0.000779 AC XY: 57 AN XY: 73184

Gnomad4 AFR AF: 0.00137

Gnomad4 AMR AF: 0.000666

Gnomad4 ASJ AF: 0.00493

Gnomad4 EAS AF: 0.000987

Gnomad4 SAS AF: 0.00189

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000462

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000551 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

ANKRD36C: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.28
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

Other links and lift over

dbSNP: rs1405209973; hg19: chr2-96568695; COSMIC: COSV54762273;