rs6527958

Variant names:

• chrX-19978386-C-T
• rs6527958
• NM_001367774.2:c.-34-8088G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367774.2(BCLAF3):​c.-34-8088G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 110,321 control chromosomes in the GnomAD database, including 8,192 homozygotes. There are 10,786 hemizygotes 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 0.35 (8192 hom., 10786 hem., cov: 22)
• Consequence: BCLAF3 NM_001367774.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 1 publications found

Genes affected

BCLAF3 (HGNC:27413): (BCLAF1 and THRAP3 family member 3) Predicted to enable DNA binding activity and transcription coregulator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in mitochondrion. Predicted to be part of mediator complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367774.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCLAF3	NM_001367774.2	MANE Select	c.-34-8088G>A		intron	N/A	NP_001354703.1	A2AJT9-1
	BCLAF3	NM_198279.4		c.-34-8088G>A		intron	N/A	NP_938020.2	A2AJT9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCLAF3	ENST00000379682.9	TSL:5 MANE Select	c.-34-8088G>A		intron	N/A	ENSP00000369004.4	A2AJT9-1
	BCLAF3	ENST00000855290.1		c.-34-8088G>A		intron	N/A	ENSP00000525349.1
	BCLAF3	ENST00000931163.1		c.-34-8088G>A		intron	N/A	ENSP00000601222.1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 38851 AN: 110267 Hom.: 8187 Cov.: 22

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0269

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.353 AC: 38914 AN: 110321 Hom.: 8192 Cov.: 22 AF XY: 0.331 AC XY: 10786 AN XY: 32607

African (AFR) AF: 0.801 AC: 24107 AN: 30106

American (AMR) AF: 0.231 AC: 2395 AN: 10386

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 585 AN: 2626

East Asian (EAS) AF: 0.0270 AC: 95 AN: 3519

South Asian (SAS) AF: 0.0748 AC: 199 AN: 2662

European-Finnish (FIN) AF: 0.200 AC: 1171 AN: 5850

Middle Eastern (MID) AF: 0.183 AC: 40 AN: 218

European-Non Finnish (NFE) AF: 0.184 AC: 9691 AN: 52772

Other (OTH) AF: 0.326 AC: 491 AN: 1504

Alfa AF: 0.287 Hom.: 2009

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.74
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6527958; hg19: chrX-19996504;