Variant X-110309439-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_015365.3(AMMECR1):c.473+8160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 111,208 control chromosomes in the GnomAD database, including 4,370 homozygotes. There are 9,667 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 4370 hom., 9667 hem., cov: 22)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

AMMECR1
NM_015365.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.693

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
AMMECR1	NM_015365.3 linkuse as main transcript	c.473+8160G>A	intron_variant	ENST00000262844.10
AMMECR1	NM_001025580.2 linkuse as main transcript	c.473+8160G>A	intron_variant
AMMECR1	NM_001171689.2 linkuse as main transcript	c.104+8160G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AMMECR1	ENST00000262844.10 linkuse as main transcript	c.473+8160G>A		intron_variant		1	NM_015365.3	A1	Q9Y4X0-1

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

31263

AN:

111160

Hom.:

4365

Cov.:

AF XY:

0.290

AC XY:

9663

AN XY:

33372

show subpopulations

Gnomad AFR

AF:

0.0514

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.929

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.330

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.321

Gnomad OTH

AF:

0.286

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.281

AC:

31264

AN:

111208

Hom.:

4370

Cov.:

AF XY:

0.289

AC XY:

9667

AN XY:

33430

show subpopulations

Gnomad4 AFR

AF:

0.0513

Gnomad4 AMR

AF:

0.429

Gnomad4 ASJ

AF:

0.224

Gnomad4 EAS

AF:

0.928

Gnomad4 SAS

AF:

0.603

Gnomad4 FIN

AF:

0.330

Gnomad4 NFE

AF:

0.321

Gnomad4 OTH

AF:

0.296

Alfa

AF:

0.325

Hom.:

9385

Bravo

AF:

0.285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.80

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over