2-97154693-C-T

Position:

• chr2-97154693-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001354587.1(ANKRD36):​c.1212C>T​(p.Asp404=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0068 (2 hom., cov: 26)
  • Exomes 𝑓: 0.000063 (15 hom.)
  • Failed GnomAD Quality Control
• Consequence: ANKRD36 NM_001354587.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.08

Genes affected

ANKRD36 (HGNC:24079): (ankyrin repeat domain 36)

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 2-97154693-C-T is Benign according to our data. Variant chr2-97154693-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651160.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.08 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD36	NM_001354587.1	c.1212C>T	p.Asp404=	synonymous_variant	15/76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD36	ENST00000420699.9	c.1212C>T	p.Asp404=	synonymous_variant	15/76	5	NM_001354587.1	ENSP00000391950	P1
ANKRD36	ENST00000461153.7	c.1212C>T	p.Asp404=	synonymous_variant	15/75	5		ENSP00000419530	P1
ANKRD36	ENST00000652721.1	c.1212C>T	p.Asp404=	synonymous_variant	15/76			ENSP00000498611	P1

Frequencies

GnomAD3 genomes AF: 0.00677 AC: 621 AN: 91674 Hom.: 2 Cov.: 26

Gnomad AFR AF: 0.00364

Gnomad AMI AF: 0.00542

Gnomad AMR AF: 0.00655

Gnomad ASJ AF: 0.00338

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.00645

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0104

Gnomad NFE AF: 0.00784

Gnomad OTH AF: 0.00610

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000628 AC: 83 AN: 1321826 Hom.: 15 Cov.: 30 AF XY: 0.0000829 AC XY: 54 AN XY: 651766

Gnomad4 AFR exome AF: 0.0000645

Gnomad4 AMR exome AF: 0.000118

Gnomad4 ASJ exome AF: 0.0000412

Gnomad4 EAS exome AF: 0.0000869

Gnomad4 SAS exome AF: 0.0000390

Gnomad4 FIN exome AF: 0.00121

Gnomad4 NFE exome AF: 0.0000301

Gnomad4 OTH exome AF: 0.0000361

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00679 AC: 623 AN: 91710 Hom.: 2 Cov.: 26 AF XY: 0.00956 AC XY: 384 AN XY: 40148

Gnomad4 AFR AF: 0.00368

Gnomad4 AMR AF: 0.00665

Gnomad4 ASJ AF: 0.00338

Gnomad4 EAS AF: 0.00704

Gnomad4 SAS AF: 0.00613

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.00787

Gnomad4 OTH AF: 0.00681

Alfa AF: 0.135 Hom.: 140

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

Dec 01, 2022

ANKRD36: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.19
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: rs776281681; hg19: chr2-97820430; COSMIC: COSV70742939;