NM_001286474.2:c.533-2570A>C

Variant names:

• chr6-32318984-T-G
• rs498422
• NM_001286474.2:c.533-2570A>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.533-2570A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,100 control chromosomes in the GnomAD database, including 2,499 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 0.14 (2499 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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.533-2570A>C		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.580+3502A>C		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.512-2570A>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.533-2570A>C		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.512-2570A>C		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.580+3502A>C		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21123 AN: 151980 Hom.: 2493 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.0751

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.00923

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.139 AC: 21154 AN: 152100 Hom.: 2499 Cov.: 32 AF XY: 0.136 AC XY: 10149 AN XY: 74370

African (AFR) AF: 0.314 AC: 13020 AN: 41424

American (AMR) AF: 0.0995 AC: 1521 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0751 AC: 260 AN: 3462

East Asian (EAS) AF: 0.177 AC: 919 AN: 5178

South Asian (SAS) AF: 0.169 AC: 816 AN: 4824

European-Finnish (FIN) AF: 0.00923 AC: 98 AN: 10616

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0602 AC: 4094 AN: 68004

Other (OTH) AF: 0.139 AC: 293 AN: 2110

Alfa AF: 0.0857 Hom.: 4063

Bravo AF: 0.151

Asia WGS AF: 0.180 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.61
PhyloP100		0.85
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: rs498422; hg19: chr6-32286761;