6-32297751-C-T

Variant names:

• chr6-32297751-C-T
• rs17422797
• NM_001286474.2:c.631+2171G>A

Variant summary

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

The ENST00000533191.6(TSBP1):​c.631+2171G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 152,140 control chromosomes in the GnomAD database, including 481 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 0.061 (481 hom., cov: 32)
• Consequence: TSBP1 ENST00000533191.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• Publications: 22 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533191.6. 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.631+2171G>A		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.637+2171G>A		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.589+2171G>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.631+2171G>A		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.610+2171G>A		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.637+2171G>A		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 9271 AN: 152022 Hom.: 480 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0610 AC: 9277 AN: 152140 Hom.: 481 Cov.: 32 AF XY: 0.0674 AC XY: 5011 AN XY: 74364

African (AFR) AF: 0.0126 AC: 522 AN: 41530

American (AMR) AF: 0.0755 AC: 1153 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00952 AC: 33 AN: 3466

East Asian (EAS) AF: 0.0839 AC: 434 AN: 5174

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4824

European-Finnish (FIN) AF: 0.204 AC: 2155 AN: 10562

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0677 AC: 4600 AN: 67992

Other (OTH) AF: 0.0398 AC: 84 AN: 2110

Alfa AF: 0.0621 Hom.: 980

Bravo AF: 0.0482

Asia WGS AF: 0.0500 AC: 174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.81
PhyloP100		-0.81
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: rs17422797; hg19: chr6-32265528;