6-32347950-T-C

Variant names:

• chr6-32347950-T-C
• rs910049
• NM_001286474.2:c.280+1790A>G

Variant summary

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

The NM_001286474.2(TSBP1):​c.280+1790A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,102 control chromosomes in the GnomAD database, including 43,930 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 0.76 (43930 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 59 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.84 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.280+1790A>G		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.349+1790A>G		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.259+1790A>G		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.280+1790A>G		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.259+1790A>G		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.349+1790A>G		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115232 AN: 151984 Hom.: 43890 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.758 AC: 115326 AN: 152102 Hom.: 43930 Cov.: 32 AF XY: 0.763 AC XY: 56759 AN XY: 74366

African (AFR) AF: 0.711 AC: 29492 AN: 41476

American (AMR) AF: 0.748 AC: 11432 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2736 AN: 3472

East Asian (EAS) AF: 0.783 AC: 4049 AN: 5170

South Asian (SAS) AF: 0.862 AC: 4149 AN: 4812

European-Finnish (FIN) AF: 0.838 AC: 8874 AN: 10586

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52001 AN: 67980

Other (OTH) AF: 0.737 AC: 1557 AN: 2114

Alfa AF: 0.770 Hom.: 166392

Bravo AF: 0.747

Asia WGS AF: 0.757 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-1.4
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: rs910049; hg19: chr6-32315727;