rs1042179

Variant names:

• chrX-75584721-G-A
• rs1042179
• ENST00000445336.2:n.1918G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-75584721-G-A
• chrX-75584721-G-T

Variant summary

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

The ENST00000445336.2(BRAFP1):​n.1918G>A variant causes a non coding transcript exon 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: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: BRAFP1 ENST00000445336.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.62
• Publications: 1 publications found

Genes affected

BRAFP1 (HGNC:18615): (BRAF pseudogene 1)

ENSG00000302260 (HGNC:):

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=-0.6).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRAFP1		n.75584721G>A		intragenic_variant
LOC107985664	XR_001755885.2	n.529-20197G>A		intron_variant	Intron 1 of 3
LOC107985664	XR_001755889.2	n.646+4983G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRAFP1	ENST00000445336.2	n.1918G>A		non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000302260	ENST00000785233.1	n.419-20197G>A		intron_variant	Intron 1 of 5
ENSG00000302260	ENST00000785234.1	n.125-20197G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 938213 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 293443

African (AFR) AF: 0.00 AC: 0 AN: 23226

American (AMR) AF: 0.00 AC: 0 AN: 34910

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18407

East Asian (EAS) AF: 0.00 AC: 0 AN: 29445

South Asian (SAS) AF: 0.00 AC: 0 AN: 50604

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40171

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2604

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 698237

Other (OTH) AF: 0.00 AC: 0 AN: 40609

GnomAD4 genome Cov.: 23

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		2.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1042179; hg19: chrX-74804556;