Variant 10-46390897-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000619162.5(ANXA8L1):c.951C>T(p.Asn317=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00373 in 1,383,090 control chromosomes in the GnomAD database, including 1,110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 36 hom., cov: 15)

Exomes 𝑓: 0.0039 ( 1074 hom. )

Consequence

ANXA8L1
ENST00000619162.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.94

Variant links:

Genes affected

ANXA8L1 (HGNC:23334): (annexin A8 like 1) This gene encodes a member of the annexin family of evolutionarily conserved Ca2+ and phospholipid binding proteins. The encoded protein may function as an an anticoagulant that indirectly inhibits the thromboplastin-specific complex. Overexpression of this gene has been associated with acute myelocytic leukemia. A highly similar duplicated copy of this gene is found in close proximity on the long arm of chromosome 10. [provided by RefSeq, Apr 2014]

ANXA8L1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 10-46390897-C-T is Benign according to our data. Variant chr10-46390897-C-T is described in ClinVar as [Benign]. Clinvar id is 2640434.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.94 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 36 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ANXA8L1	NM_001098845.3 linkuse as main transcript	c.951C>T	p.Asn317=	synonymous_variant	12/12	ENST00000619162.5	NP_001092315.2
ANXA8L1	NM_001278924.2 linkuse as main transcript	c.798C>T	p.Asn266=	synonymous_variant	9/9		NP_001265853.1
ANXA8L1	NM_001278923.2 linkuse as main transcript	c.780C>T	p.Asn260=	synonymous_variant	10/10		NP_001265852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANXA8L1	ENST00000619162.5 linkuse as main transcript	c.951C>T	p.Asn317=	synonymous_variant	12/12	1	NM_001098845.3	ENSP00000480221	P1	Q5VT79-1

Frequencies

GnomAD3 genomes

AF:

0.00226

AC:

235

AN:

103994

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000499

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00103

Gnomad ASJ

AF:

0.00539

Gnomad EAS

AF:

0.000202

Gnomad SAS

AF:

0.000285

Gnomad FIN

AF:

0.000594

Gnomad MID

AF:

0.0126

Gnomad NFE

AF:

0.00393

Gnomad OTH

AF:

0.00217

GnomAD3 exomes

AF:

0.00527

AC:

1162

AN:

220414

Hom.:

218

AF XY:

0.00555

AC XY:

658

AN XY:

118640

show subpopulations

Gnomad AFR exome

AF:

0.000194

Gnomad AMR exome

AF:

0.00284

Gnomad ASJ exome

AF:

0.0366

Gnomad EAS exome

AF:

0.000165

Gnomad SAS exome

AF:

0.00173

Gnomad FIN exome

AF:

0.00136

Gnomad NFE exome

AF:

0.00664

Gnomad OTH exome

AF:

0.00808

GnomAD4 exome

AF:

0.00385

AC:

4929

AN:

1278982

Hom.:

1074

Cov.:

AF XY:

0.00383

AC XY:

2430

AN XY:

634486

show subpopulations

Gnomad4 AFR exome

AF:

0.000417

Gnomad4 AMR exome

AF:

0.00154

Gnomad4 ASJ exome

AF:

0.0176

Gnomad4 EAS exome

AF:

0.0000509

Gnomad4 SAS exome

AF:

0.00114

Gnomad4 FIN exome

AF:

0.00105

Gnomad4 NFE exome

AF:

0.00423

Gnomad4 OTH exome

AF:

0.00432

GnomAD4 genome

AF:

0.00226

AC:

235

AN:

104108

Hom.:

Cov.:

AF XY:

0.00205

AC XY:

103

AN XY:

50346

show subpopulations

Gnomad4 AFR

AF:

0.000497

Gnomad4 AMR

AF:

0.00103

Gnomad4 ASJ

AF:

0.00539

Gnomad4 EAS

AF:

0.000202

Gnomad4 SAS

AF:

0.000285

Gnomad4 FIN

AF:

0.000594

Gnomad4 NFE

AF:

0.00393

Gnomad4 OTH

AF:

0.00214

Alfa

AF:

0.00386

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2023

ANXA8L1: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

6.3

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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