chr12-111685480-A-T

Variant names:

• chr12-111685480-A-T
• rs601663
• NM_006768.5:c.82+231T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006768.5(BRAP):​c.82+231T>A variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BRAP NM_006768.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 24 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRAP	NM_006768.5	c.82+231T>A		intron_variant	Intron 1 of 11	ENST00000419234.9	NP_006759.3
BRAP	XM_005253944.5	c.205+108T>A		intron_variant	Intron 1 of 11		XP_005254001.1
BRAP	XM_017019992.2	c.82+231T>A		intron_variant	Intron 1 of 10		XP_016875481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRAP	ENST00000419234.9	c.82+231T>A		intron_variant	Intron 1 of 11	1	NM_006768.5	ENSP00000403524.3
BRAP	ENST00000327551.6	c.-9+108T>A		intron_variant	Intron 1 of 11	1		ENSP00000330813.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 860686 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 416838

African (AFR) AF: 0.00 AC: 0 AN: 17648

American (AMR) AF: 0.00 AC: 0 AN: 10384

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12628

East Asian (EAS) AF: 0.00 AC: 0 AN: 23204

South Asian (SAS) AF: 0.00 AC: 0 AN: 33844

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21652

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2384

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 702832

Other (OTH) AF: 0.00 AC: 0 AN: 36110

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.5
DANN	Benign	0.37
PhyloP100		-0.0060
PromoterAI		-0.027	Neutral

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

Other links and lift over

dbSNP: rs601663; hg19: chr12-112123284;