rs10747493

Variant names:

• chr1-91992286-C-A
• rs10747493
• NM_207189.4:c.2087C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-91992286-C-A
• chr1-91992286-C-G
• chr1-91992286-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_207189.4(BRDT):​c.2087C>A​(p.Pro696Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P696L) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BRDT NM_207189.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

Genes affected

BRDT (HGNC:1105): (bromodomain testis associated) BRDT is similar to the RING3 protein family. It possesses 2 bromodomain motifs and a PEST sequence (a cluster of proline, glutamic acid, serine, and threonine residues), characteristic of proteins that undergo rapid intracellular degradation. The bromodomain is found in proteins that regulate transcription. Several transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05376783).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRDT	NM_207189.4	c.2087C>A	p.Pro696Gln	missense_variant	Exon 14 of 19	ENST00000399546.7	NP_997072.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRDT	ENST00000399546.7	c.2087C>A	p.Pro696Gln	missense_variant	Exon 14 of 19	2	NM_207189.4	ENSP00000387822.3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1354248 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 673684

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.29
DANN	Benign	0.11
DEOGEN2	Benign	0.067	T;.;.;.;T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.0026	N
LIST_S2	Benign	0.18	.;T;T;T;T
M_CAP	Benign	0.0019	T
MetaRNN	Benign	0.054	T;T;T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	-0.34	N;.;.;.;N
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-0.42	N;N;N;.;N
REVEL	Benign	0.014
Sift	Benign	0.14	T;T;T;.;T
Sift4G	Benign	0.19	T;T;T;T;T
Polyphen		0.0	B;.;.;.;B
Vest4		0.078
MutPred		0.17		Loss of helix (P = 0.0123);.;.;.;Loss of helix (P = 0.0123);
MVP		0.30
MPC		0.074
ClinPred		0.047	T
GERP RS		0.031
Varity_R		0.025
gMVP		0.11

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

Other links and lift over

dbSNP: rs10747493; hg19: chr1-92457843;