Menu
GeneBe

9-842051-G-A

Variant summary

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

The NM_021951.3(DMRT1):c.213G>A(p.Pro71=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00066 in 1,545,406 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00056 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00067 ( 2 hom. )

Consequence

DMRT1
NM_021951.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.154
Variant links:
Genes affected
DMRT1 (HGNC:2934): (doublesex and mab-3 related transcription factor 1) This gene is found in a cluster with two other members of the gene family, having in common a zinc finger-like DNA-binding motif (DM domain). The DM domain is an ancient, conserved component of the vertebrate sex-determining pathway that is also a key regulator of male development in flies and nematodes. This gene exhibits a gonad-specific and sexually dimorphic expression pattern. Defective testicular development and XY feminization occur when this gene is hemizygous. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 9-842051-G-A is Benign according to our data. Variant chr9-842051-G-A is described in ClinVar as [Benign]. Clinvar id is 1598990.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.154 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 86 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DMRT1NM_021951.3 linkuse as main transcriptc.213G>A p.Pro71= synonymous_variant 1/5 ENST00000382276.8
DMRT1XM_006716732.2 linkuse as main transcriptc.213G>A p.Pro71= synonymous_variant 1/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DMRT1ENST00000382276.8 linkuse as main transcriptc.213G>A p.Pro71= synonymous_variant 1/51 NM_021951.3 P1Q9Y5R6-1
DMRT1ENST00000564322.1 linkuse as main transcriptn.362G>A non_coding_transcript_exon_variant 1/31

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000565
AC:
86
AN:
152132
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000654
Gnomad ASJ
AF:
0.00634
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00394
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.000441
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.00110
AC:
155
AN:
141314
Hom.:
1
AF XY:
0.00131
AC XY:
101
AN XY:
77136
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000283
Gnomad ASJ exome
AF:
0.00605
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000337
Gnomad OTH exome
AF:
0.00119
GnomAD4 exome
AF:
0.000671
AC:
935
AN:
1393156
Hom.:
2
Cov.:
35
AF XY:
0.000762
AC XY:
524
AN XY:
687918
show subpopulations
Gnomad4 AFR exome
AF:
0.000220
Gnomad4 AMR exome
AF:
0.000333
Gnomad4 ASJ exome
AF:
0.00564
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00319
Gnomad4 FIN exome
AF:
0.0000245
Gnomad4 NFE exome
AF:
0.000387
Gnomad4 OTH exome
AF:
0.00114
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000558
AC:
85
AN:
152250
Hom.:
0
Cov.:
32
AF XY:
0.000591
AC XY:
44
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000653
Gnomad4 ASJ
AF:
0.00634
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00373
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000441
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000797
Hom.:
0
Bravo
AF:
0.000416
Asia WGS
AF:
0.000866
AC:
3
AN:
3478

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 submitterclinical testingInvitaeMar 09, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
10
Dann
Benign
0.94

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.

Other links and lift over

dbSNP: rs376518776; hg19: chr9-842051; API