NM_001286474.2:c.281-1047T>C

Variant names:

• chr6-32344305-A-G
• rs6904320
• NM_001286474.2:c.281-1047T>C

Variant summary

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

The NM_001286474.2(TSBP1):​c.281-1047T>C 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 0.76 (39227 hom., cov: 17)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 28 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.839 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.281-1047T>C		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.350-4667T>C		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.260-1047T>C		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.281-1047T>C		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.260-1047T>C		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.350-4667T>C		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.756 AC: 102896 AN: 136164 Hom.: 39194 Cov.: 17

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.756 AC: 102980 AN: 136276 Hom.: 39227 Cov.: 17 AF XY: 0.760 AC XY: 49670 AN XY: 65340

African (AFR) AF: 0.699 AC: 24540 AN: 35116

American (AMR) AF: 0.748 AC: 10050 AN: 13440

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2665 AN: 3380

East Asian (EAS) AF: 0.785 AC: 3539 AN: 4506

South Asian (SAS) AF: 0.863 AC: 3505 AN: 4060

European-Finnish (FIN) AF: 0.837 AC: 6416 AN: 7664

Middle Eastern (MID) AF: 0.817 AC: 232 AN: 284

European-Non Finnish (NFE) AF: 0.767 AC: 49878 AN: 65064

Other (OTH) AF: 0.735 AC: 1382 AN: 1880

Alfa AF: 0.770 Hom.: 123011

Asia WGS AF: 0.753 AC: 2616 AN: 3472

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	0.61
PhyloP100		-0.68
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: rs6904320; hg19: chr6-32312082;