Variant 2-97224796-A-AT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PVS1_ModerateBP6_Moderate

The NM_001354587.1(ANKRD36):c.3878-3dupT variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.049 ( 379 hom., cov: 29)

Exomes 𝑓: 0.0032 ( 403 hom. )

Failed GnomAD Quality Control

Consequence

ANKRD36
NM_001354587.1 splice_acceptor, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0630

Variant links:

Genes affected

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

ANKRD36 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.012874044 fraction of the gene. Cryptic splice site detected, with MaxEntScore 4, offset of 0 (no position change), new splice context is: aaatatataattttttttAGcag. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.

BP6

Variant 2-97224796-A-AT is Benign according to our data. Variant chr2-97224796-A-AT is described in ClinVar as [Benign]. Clinvar id is 2858945.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1 link	c.3878-3dupT		splice_acceptor_variant, intron_variant	Intron 66 of 75	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ANKRD36	ENST00000420699.9 link	c.3878-10_3878-9insT	intron_variant	Intron 66 of 75	5	NM_001354587.1	ENSP00000391950.4	A6QL64-1
ANKRD36	ENST00000461153.7 link	c.3878-10_3878-9insT	intron_variant	Intron 66 of 74	5		ENSP00000419530.3	A6QL64-1
ANKRD36	ENST00000652721.1 link	c.3878-10_3878-9insT	intron_variant	Intron 66 of 75			ENSP00000498611.1	A6QL64-1
ANKRD36	ENST00000421946.2 link	n.1101-13_1101-12insT	intron_variant	Intron 8 of 13	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

5358

AN:

108458

Hom.:

378

Cov.:

FAILED QC

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.0131

Gnomad AMR

AF:

0.0345

Gnomad ASJ

AF:

0.0294

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.000826

Gnomad MID

AF:

0.0229

Gnomad NFE

AF:

0.00938

Gnomad OTH

AF:

0.0459

GnomAD3 exomes

AF:

0.0000165

AC:

AN:

60614

Hom.:

AF XY:

0.0000334

AC XY:

AN XY:

29978

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:

0.000320

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00325

AC:

3677

AN:

1131540

Hom.:

403

Cov.:

AF XY:

0.00365

AC XY:

2031

AN XY:

556388

show subpopulations

Gnomad4 AFR exome

AF:

0.0342

Gnomad4 AMR exome

AF:

0.0187

Gnomad4 ASJ exome

AF:

0.00794

Gnomad4 EAS exome

AF:

0.0228

Gnomad4 SAS exome

AF:

0.0211

Gnomad4 FIN exome

AF:

0.000797

Gnomad4 NFE exome

AF:

0.00120

Gnomad4 OTH exome

AF:

0.00478

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0494

AC:

5361

AN:

108502

Hom.:

379

Cov.:

AF XY:

0.0465

AC XY:

2454

AN XY:

52812

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.0345

Gnomad4 ASJ

AF:

0.0294

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.111

Gnomad4 FIN

AF:

0.000826

Gnomad4 NFE

AF:

0.00936

Gnomad4 OTH

AF:

0.0472

Alfa

AF:

0.00730

Hom.:

Asia WGS

AF:

0.335

AC:

885

AN:

2648

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 02, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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