rs7136874

chr12-111675854-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006768.5(BRAP):c.634-3080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,756 control chromosomes in the GnomAD database, including 14,286 homozygotes. 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 0.36 (14286 hom., cov: 30)
• Consequence: BRAP NM_006768.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679

Genes affected

BRAP (HGNC:1099): (BRCA1 associated protein) The protein encoded by this gene was identified by its ability to bind to the nuclear localization signal of BRCA1 and other proteins. It is a cytoplasmic protein which may regulate nuclear targeting by retaining proteins with a nuclear localization signal in the cytoplasm. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRAP	NM_006768.5	c.634-3080G>A		intron_variant		ENST00000419234.9
BRAP	XM_005253944.5	c.757-3080G>A		intron_variant
BRAP	XM_017019992.2	c.472-3080G>A		intron_variant
BRAP	XM_047429622.1	c.187-3080G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRAP	ENST00000419234.9	c.634-3080G>A		intron_variant		1	NM_006768.5	P1
BRAP	ENST00000327551.6	c.544-3080G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54337 AN: 151638 Hom.: 14247 Cov.: 30

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.338

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.359 AC: 54439 AN: 151756 Hom.: 14286 Cov.: 30 AF XY: 0.359 AC XY: 26648 AN XY: 74140

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.335

Alfa AF: 0.280 Hom.: 1858

Bravo AF: 0.392

Asia WGS AF: 0.553 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.17
Dann	Benign	0.57

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: rs7136874; hg19: chr12-112113658;