6-32369853-G-A

Variant names:

• chr6-32369853-G-A
• rs2273017
• NM_001286474.2:c.100+44C>T

Variant summary

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

The NM_001286474.2(TSBP1):​c.100+44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 1,213,680 control chromosomes in the GnomAD database, including 206,252 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 0.50 (20856 hom., cov: 31)
  • Exomes 𝑓: 0.59 (185396 hom.)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 59 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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.100+44C>T		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.100+44C>T		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.100+44C>T		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.100+44C>T		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.100+44C>T		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.100+44C>T		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76497 AN: 151856 Hom.: 20835 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.512

GnomAD2 exomes AF: 0.589 AC: 144967 AN: 246278 AF XY: 0.595

Gnomad AFR exome AF: 0.279

Gnomad AMR exome AF: 0.629

Gnomad ASJ exome AF: 0.636

Gnomad EAS exome AF: 0.621

Gnomad FIN exome AF: 0.560

Gnomad NFE exome AF: 0.608

Gnomad OTH exome AF: 0.569

GnomAD4 exome AF: 0.587 AC: 623189 AN: 1061704 Hom.: 185396 Cov.: 14 AF XY: 0.590 AC XY: 322402 AN XY: 546028

African (AFR) AF: 0.279 AC: 7153 AN: 25656

American (AMR) AF: 0.619 AC: 27375 AN: 44222

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 14957 AN: 23686

East Asian (EAS) AF: 0.562 AC: 21298 AN: 37884

South Asian (SAS) AF: 0.614 AC: 47953 AN: 78072

European-Finnish (FIN) AF: 0.561 AC: 29266 AN: 52128

Middle Eastern (MID) AF: 0.636 AC: 3163 AN: 4970

European-Non Finnish (NFE) AF: 0.594 AC: 444594 AN: 747946

Other (OTH) AF: 0.582 AC: 27430 AN: 47140

GnomAD4 genome AF: 0.504 AC: 76550 AN: 151976 Hom.: 20856 Cov.: 31 AF XY: 0.504 AC XY: 37436 AN XY: 74278

African (AFR) AF: 0.278 AC: 11501 AN: 41430

American (AMR) AF: 0.541 AC: 8267 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2195 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3230 AN: 5158

South Asian (SAS) AF: 0.596 AC: 2872 AN: 4820

European-Finnish (FIN) AF: 0.562 AC: 5930 AN: 10548

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40744 AN: 67952

Other (OTH) AF: 0.512 AC: 1080 AN: 2110

Alfa AF: 0.588 Hom.: 97762

Bravo AF: 0.493

Asia WGS AF: 0.566 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-1.3
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: rs2273017; hg19: chr6-32337630; COSMIC: COSV66659056;