ENST00000445336.2:n.1918G>T

Variant names:

• chrX-75584721-G-T
• rs1042179
• ENST00000445336.2:n.1918G>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>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000381 in 1,050,124 control chromosomes in the GnomAD database, including 1 homozygotes. There are no hemizygote samples in GnomAD. 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 0.0000089 (0 hom., 0 hem., cov: 23)
  • Exomes 𝑓: 0.0000032 (1 hom. 0 hem.)
• 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445336.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRAFP1	ENST00000445336.2	TSL:6	n.1918G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000302260	ENST00000785233.1		n.419-20197G>T		intron	N/A
	ENSG00000302260	ENST00000785234.1		n.125-20197G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000894 AC: 1 AN: 111911 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000188

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000320 AC: 3 AN: 938213 Hom.: 1 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 293443

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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: 0.00000143 AC: 1 AN: 698237

Other (OTH) AF: 0.0000493 AC: 2 AN: 40609

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.00000894 AC: 1 AN: 111911 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 34073

African (AFR) AF: 0.00 AC: 0 AN: 30785

American (AMR) AF: 0.00 AC: 0 AN: 10577

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2640

East Asian (EAS) AF: 0.00 AC: 0 AN: 3577

South Asian (SAS) AF: 0.00 AC: 0 AN: 2651

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6025

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 240

European-Non Finnish (NFE) AF: 0.0000188 AC: 1 AN: 53224

Other (OTH) AF: 0.00 AC: 0 AN: 1510

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.0
DANN	Benign	0.35
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;