chr6-32319790-G-A

Variant names:

• chr6-32319790-G-A
• rs9268230
• NM_001286474.2:c.532+2696C>T

Variant summary

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

The NM_001286474.2(TSBP1):​c.532+2696C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,006 control chromosomes in the GnomAD database, including 35,671 homozygotes. 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 0.69 (35671 hom., cov: 30)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 12 publications found

Genes affected

TSBP1 (HGNC:13922): (testis expressed basic protein 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286474.2. 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
	TSBP1	NM_001286474.2	MANE Select	c.532+2696C>T		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.580+2696C>T		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.511+2696C>T		intron	N/A	NP_001273404.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	ENST00000533191.6	TSL:1 MANE Select	c.532+2696C>T		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.511+2696C>T		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.580+2696C>T		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103363 AN: 150888 Hom.: 35638 Cov.: 30

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.685 AC: 103445 AN: 151006 Hom.: 35671 Cov.: 30 AF XY: 0.683 AC XY: 50381 AN XY: 73734

African (AFR) AF: 0.686 AC: 28148 AN: 41036

American (AMR) AF: 0.671 AC: 10158 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2599 AN: 3462

East Asian (EAS) AF: 0.774 AC: 3908 AN: 5052

South Asian (SAS) AF: 0.816 AC: 3891 AN: 4770

European-Finnish (FIN) AF: 0.609 AC: 6397 AN: 10510

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.679 AC: 46010 AN: 67758

Other (OTH) AF: 0.692 AC: 1440 AN: 2080

Alfa AF: 0.693 Hom.: 7406

Bravo AF: 0.689

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.50
PhyloP100		-1.2
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: rs9268230; hg19: chr6-32287567;