Variant 12-53424503-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020547.3(AMHR2):c.232+33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 1,604,202 control chromosomes in the GnomAD database, including 9,301 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 4866 hom., cov: 32)

Exomes 𝑓: 0.015 ( 4435 hom. )

Consequence

AMHR2
NM_020547.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.177

Variant links:

Genes affected

AMHR2 (HGNC:465): (anti-Mullerian hormone receptor type 2) This gene encodes the receptor for the anti-Mullerian hormone (AMH) which, in addition to testosterone, results in male sex differentiation. AMH and testosterone are produced in the testes by different cells and have different effects. Testosterone promotes the development of male genitalia while the binding of AMH to the encoded receptor prevents the development of the mullerian ducts into uterus and Fallopian tubes. Mutations in this gene are associated with persistent Mullerian duct syndrome type II. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Sep 2009]

AMHR2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 12-53424503-A-G is Benign according to our data. Variant chr12-53424503-A-G is described in ClinVar as [Benign]. Clinvar id is 1269702.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AMHR2	NM_020547.3 linkuse as main transcript	c.232+33A>G		intron_variant		ENST00000257863.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
AMHR2	ENST00000257863.9 linkuse as main transcript	c.232+33A>G	intron_variant	1	NM_020547.3	P1	Q16671-1
AMHR2	ENST00000379791.7 linkuse as main transcript	c.232+33A>G	intron_variant	1			Q16671-3
AMHR2	ENST00000550311.5 linkuse as main transcript	c.232+33A>G	intron_variant	1			Q16671-2
AMHR2	ENST00000553037.1 linkuse as main transcript	n.193+33A>G	intron_variant, non_coding_transcript_variant	4

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20869

AN:

151958

Hom.:

4840

Cov.:

show subpopulations

Gnomad AFR

AF:

0.475

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0557

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00249

Gnomad OTH

AF:

0.0939

GnomAD3 exomes

AF:

0.0366

AC:

8487

AN:

232010

Hom.:

1812

AF XY:

0.0266

AC XY:

3327

AN XY:

125108

show subpopulations

Gnomad AFR exome

AF:

0.496

Gnomad AMR exome

AF:

0.0276

Gnomad ASJ exome

AF:

0.00450

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000966

Gnomad FIN exome

AF:

0.000296

Gnomad NFE exome

AF:

0.00212

Gnomad OTH exome

AF:

0.0195

GnomAD4 exome

AF:

0.0153

AC:

22237

AN:

1452126

Hom.:

4435

Cov.:

AF XY:

0.0132

AC XY:

9538

AN XY:

721430

show subpopulations

Gnomad4 AFR exome

AF:

0.501

Gnomad4 AMR exome

AF:

0.0317

Gnomad4 ASJ exome

AF:

0.00426

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00113

Gnomad4 FIN exome

AF:

0.000283

Gnomad4 NFE exome

AF:

0.00155

Gnomad4 OTH exome

AF:

0.0338

GnomAD4 genome

AF:

0.138

AC:

20952

AN:

152076

Hom.:

4866

Cov.:

AF XY:

0.133

AC XY:

9894

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.0556

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00249

Gnomad4 OTH

AF:

0.0929

Alfa

AF:

0.0949

Hom.:

528

Bravo

AF:

0.158

Asia WGS

AF:

0.0340

AC:

117

AN:

3478

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	GeneDx	Jun 19, 2021	- -
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

-0.84

CADD

Benign

5.2

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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