6-32353227-C-T

Variant names:

• chr6-32353227-C-T
• rs2022544
• NM_001286474.2:c.259+1897G>A

Variant summary

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

The NM_001286474.2(TSBP1):​c.259+1897G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,812 control chromosomes in the GnomAD database, including 2,185 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 0.15 (2185 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 25 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)

RNU6-603P (HGNC:47566): (RNA, U6 small nuclear 603, pseudogene)

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 (EAS) allele frequency at 95% confidence interval = 0.277 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.259+1897G>A		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.259+1897G>A		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.238+1897G>A		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.259+1897G>A		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.238+1897G>A		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.259+1897G>A		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23273 AN: 151694 Hom.: 2181 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.153 AC: 23295 AN: 151812 Hom.: 2185 Cov.: 32 AF XY: 0.166 AC XY: 12303 AN XY: 74198

African (AFR) AF: 0.122 AC: 5075 AN: 41470

American (AMR) AF: 0.132 AC: 2008 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1495 AN: 5170

South Asian (SAS) AF: 0.186 AC: 899 AN: 4828

European-Finnish (FIN) AF: 0.369 AC: 3886 AN: 10518

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9170 AN: 67782

Other (OTH) AF: 0.128 AC: 269 AN: 2104

Alfa AF: 0.136 Hom.: 3328

Bravo AF: 0.132

Asia WGS AF: 0.231 AC: 799 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.5
DANN	Benign	0.68
PhyloP100		-0.55
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: rs2022544; hg19: chr6-32321004;