6-32341131-G-A

Variant names:

• chr6-32341131-G-A
• rs9469099
• NM_001286474.2:c.302-1493C>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.302-1493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0466 in 152,106 control chromosomes in the GnomAD database, including 246 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 0.047 (246 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905
• Publications: 27 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 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.302-1493C>T		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.350-1493C>T		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.281-1493C>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.302-1493C>T		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.281-1493C>T		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.350-1493C>T		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.0466 AC: 7087 AN: 151988 Hom.: 248 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0466 AC: 7084 AN: 152106 Hom.: 246 Cov.: 32 AF XY: 0.0494 AC XY: 3675 AN XY: 74362

African (AFR) AF: 0.0688 AC: 2855 AN: 41468

American (AMR) AF: 0.0194 AC: 296 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3468

East Asian (EAS) AF: 0.155 AC: 802 AN: 5168

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4824

European-Finnish (FIN) AF: 0.0767 AC: 811 AN: 10576

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0278 AC: 1890 AN: 68008

Other (OTH) AF: 0.0431 AC: 91 AN: 2110

Alfa AF: 0.0347 Hom.: 346

Bravo AF: 0.0429

Asia WGS AF: 0.0980 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-0.91
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: rs9469099; hg19: chr6-32308908;