Variant chrX-110198562-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_015365.3(AMMECR1):c.960T>C(p.Asn320Asn) variant causes a synonymous change. The variant allele was found at a frequency of 0.00508 in 1,200,325 control chromosomes in the GnomAD database, including 9 homozygotes. There are 1,858 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., 75 hem., cov: 22)

Exomes 𝑓: 0.0053 ( 8 hom. 1783 hem. )

Consequence

AMMECR1
NM_015365.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.75

Variant links:

Genes affected

AMMECR1 (HGNC:467): (AMMECR nuclear protein 1) The exact function of this gene is not known, however, submicroscopic deletion of the X chromosome including this gene, COL4A5, and FACL4 genes, result in a contiguous gene deletion syndrome, the AMME complex (Alport syndrome, mental retardation, midface hypoplasia, and elliptocytosis). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

AMMECR1 links:

AMMECR1 (HGNC:):

AMMECR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant X-110198562-A-G is Benign according to our data. Variant chrX-110198562-A-G is described in ClinVar as [Benign]. Clinvar id is 779292.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Hemizygotes in GnomAd4 at 75 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
AMMECR1	NM_015365.3 linkuse as main transcript	c.960T>C	p.Asn320Asn	synonymous_variant	6/6	ENST00000262844.10	NP_056180.1
AMMECR1	NM_001025580.2 linkuse as main transcript	c.849T>C	p.Asn283Asn	synonymous_variant	5/5		NP_001020751.1
AMMECR1	NM_001171689.2 linkuse as main transcript	c.591T>C	p.Asn197Asn	synonymous_variant	8/8		NP_001165160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMMECR1	ENST00000262844.10 linkuse as main transcript	c.960T>C	p.Asn320Asn	synonymous_variant	6/6	1	NM_015365.3	ENSP00000262844.5		Q9Y4X0-1

Frequencies

GnomAD3 genomes

AF:

0.00276

AC:

308

AN:

111769

Hom.:

Cov.:

AF XY:

0.00221

AC XY:

AN XY:

33949

show subpopulations

Gnomad AFR

AF:

0.000358

Gnomad AMI

AF:

0.00146

Gnomad AMR

AF:

0.000474

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00230

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00520

Gnomad OTH

AF:

0.000664

GnomAD3 exomes

AF:

0.00284

AC:

478

AN:

168581

Hom.:

AF XY:

0.00273

AC XY:

149

AN XY:

54533

show subpopulations

Gnomad AFR exome

AF:

0.000636

Gnomad AMR exome

AF:

0.000510

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00332

Gnomad NFE exome

AF:

0.00517

Gnomad OTH exome

AF:

0.00342

GnomAD4 exome

AF:

0.00532

AC:

5788

AN:

1088556

Hom.:

Cov.:

AF XY:

0.00502

AC XY:

1783

AN XY:

355384

show subpopulations

Gnomad4 AFR exome

AF:

0.000770

Gnomad4 AMR exome

AF:

0.000643

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00432

Gnomad4 NFE exome

AF:

0.00645

Gnomad4 OTH exome

AF:

0.00372

GnomAD4 genome

AF:

0.00276

AC:

308

AN:

111769

Hom.:

Cov.:

AF XY:

0.00221

AC XY:

AN XY:

33949

show subpopulations

Gnomad4 AFR

AF:

0.000358

Gnomad4 AMR

AF:

0.000474

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00230

Gnomad4 NFE

AF:

0.00520

Gnomad4 OTH

AF:

0.000664

Alfa

AF:

0.00342

Hom.:

Bravo

AF:

0.00264

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

7.2

DANN

Benign

0.64

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.

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