NM_001286474.2:c.280+1863C>G

Variant names:

• chr6-32347877-G-C
• rs910050
• NM_001286474.2:c.280+1863C>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+1863C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,942 control chromosomes in the GnomAD database, including 14,382 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 0.42 (14382 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• 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 (AFR) allele frequency at 95% confidence interval = 0.539 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+1863C>G		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.349+1863C>G		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.259+1863C>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+1863C>G		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.259+1863C>G		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.349+1863C>G		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63960 AN: 151824 Hom.: 14358 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.421 AC: 64026 AN: 151942 Hom.: 14382 Cov.: 31 AF XY: 0.426 AC XY: 31653 AN XY: 74292

African (AFR) AF: 0.545 AC: 22549 AN: 41378

American (AMR) AF: 0.302 AC: 4614 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2127 AN: 5166

South Asian (SAS) AF: 0.433 AC: 2085 AN: 4810

European-Finnish (FIN) AF: 0.541 AC: 5707 AN: 10546

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24828 AN: 67962

Other (OTH) AF: 0.384 AC: 811 AN: 2112

Alfa AF: 0.374 Hom.: 6100

Bravo AF: 0.405

Asia WGS AF: 0.413 AC: 1436 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	3.4
DANN	Benign	0.77
PhyloP100		-0.44
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: rs910050; hg19: chr6-32315654;