X-151666660-A-T

Variant names:

• chrX-151666660-A-T
• rs5924663
• NM_173493.3:c.1071+2312A>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_173493.3(PASD1):​c.1071+2312A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 1.0 (35096 hom., 10846 hem., cov: 11)
  • Failed GnomAD Quality Control
• Consequence: PASD1 NM_173493.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 1 publications found

Genes affected

PASD1 (HGNC:20686): (PAS domain containing repressor 1) This gene encodes a protein that is thought to function as a transcription factor. The protein is a cancer-associated antigen that can stimulate autologous T-cell responses, and it is therefore considered to be a potential immunotherapeutic target for the treatment of various hematopoietic malignancies, including diffuse large B-cell lymphoma. [provided by RefSeq, May 2010]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173493.3. 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
	PASD1	NM_173493.3	MANE Select	c.1071+2312A>T		intron	N/A	NP_775764.2	Q8IV76-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PASD1	ENST00000370357.5	TSL:1 MANE Select	c.1071+2312A>T		intron	N/A	ENSP00000359382.4	Q8IV76-1
	PASD1	ENST00000464219.1	TSL:2	n.1209+2312A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 1.00 AC: 81019 AN: 81021 Hom.: 35101 Cov.: 11

Gnomad AFR AF: 1.00

Gnomad AMI AF: 1.00

Gnomad AMR AF: 1.00

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 1.00

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 1.00 AC: 81040 AN: 81042 Hom.: 35096 Cov.: 11 AF XY: 1.00 AC XY: 10846 AN XY: 10846

African (AFR) AF: 1.00 AC: 21340 AN: 21340

American (AMR) AF: 1.00 AC: 6603 AN: 6603

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2159 AN: 2159

East Asian (EAS) AF: 1.00 AC: 2563 AN: 2563

South Asian (SAS) AF: 1.00 AC: 1319 AN: 1319

European-Finnish (FIN) AF: 1.00 AC: 2828 AN: 2828

Middle Eastern (MID) AF: 1.00 AC: 184 AN: 184

European-Non Finnish (NFE) AF: 1.00 AC: 42530 AN: 42532

Other (OTH) AF: 1.00 AC: 976 AN: 976

Alfa AF: 1.00 Hom.: 8149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.24
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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: rs5924663; hg19: chrX-150835132;