Genetic Variant AMHR2:c.49+149T>A (chr12-53424132-T-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_020547.3(AMHR2):c.49+149T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,305,880 control chromosomes in the GnomAD database, including 13,239 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1168 hom., cov: 32)

Exomes 𝑓: 0.14 ( 12071 hom. )

Consequence

AMHR2
NM_020547.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0300

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=-0.69).

BP6

Variant 12-53424132-T-A is Benign according to our data. Variant chr12-53424132-T-A is described in ClinVar as [Benign]. Clinvar id is 1233614.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMHR2	NM_020547.3 link	c.49+149T>A		intron_variant	Intron 1 of 10	ENST00000257863.9	NP_065434.1	Q16671-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
AMHR2	ENST00000257863.9 link	c.49+149T>A	intron_variant	Intron 1 of 10	1	NM_020547.3	ENSP00000257863.3	Q16671-1
AMHR2	ENST00000379791.7 link	c.49+149T>A	intron_variant	Intron 1 of 8	1		ENSP00000369117.3	Q16671-3
AMHR2	ENST00000550311.5 link	c.49+149T>A	intron_variant	Intron 1 of 10	1		ENSP00000446661.1	Q16671-2
AMHR2	ENST00000553037.1 link	n.-146T>A	upstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17276

AN:

152146

Hom.:

1168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0576

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.0853

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.0476

Gnomad SAS

AF:

0.0675

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.107

GnomAD4 exome

AF:

0.138

AC:

159595

AN:

1153616

Hom.:

12071

Cov.:

AF XY:

0.137

AC XY:

79823

AN XY:

583602

show subpopulations

Gnomad4 AFR exome

AF:

0.0522

Gnomad4 AMR exome

AF:

0.0695

Gnomad4 ASJ exome

AF:

0.143

Gnomad4 EAS exome

AF:

0.0603

Gnomad4 SAS exome

AF:

0.0735

Gnomad4 FIN exome

AF:

0.129

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.128

GnomAD4 genome

AF:

0.113

AC:

17272

AN:

152264

Hom.:

1168

Cov.:

AF XY:

0.111

AC XY:

8244

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0575

Gnomad4 AMR

AF:

0.0852

Gnomad4 ASJ

AF:

0.122

Gnomad4 EAS

AF:

0.0477

Gnomad4 SAS

AF:

0.0675

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.158

Gnomad4 OTH

AF:

0.106

Alfa

AF:

0.130

Hom.:

170

Bravo

AF:

0.106

Asia WGS

AF:

0.0680

AC:

235

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

6.6

DANN

Benign

0.78

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