rs6935269

Variant names:

• chr6-32292573-T-C
• rs6935269
• ENST00000442822.6:c.1359+714A>G

Variant summary

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

The ENST00000442822.6(TSBP1):​c.1359+714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 179,170 control chromosomes in the GnomAD database, including 5,781 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 0.25 (5130 hom., cov: 32)
  • Exomes 𝑓: 0.21 (651 hom.)
• Consequence: TSBP1 ENST00000442822.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 32 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.*408A>G		downstream_gene_variant		ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.*408A>G		downstream_gene_variant		1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37969 AN: 151952 Hom.: 5117 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.206 AC: 5596 AN: 27100 Hom.: 651 AF XY: 0.202 AC XY: 2860 AN XY: 14136

African (AFR) AF: 0.325 AC: 272 AN: 838

American (AMR) AF: 0.126 AC: 236 AN: 1870

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 94 AN: 846

East Asian (EAS) AF: 0.197 AC: 252 AN: 1278

South Asian (SAS) AF: 0.171 AC: 211 AN: 1236

European-Finnish (FIN) AF: 0.306 AC: 229 AN: 748

Middle Eastern (MID) AF: 0.0896 AC: 12 AN: 134

European-Non Finnish (NFE) AF: 0.214 AC: 3955 AN: 18512

Other (OTH) AF: 0.205 AC: 335 AN: 1638

GnomAD4 genome AF: 0.250 AC: 38016 AN: 152070 Hom.: 5130 Cov.: 32 AF XY: 0.249 AC XY: 18487 AN XY: 74340

African (AFR) AF: 0.335 AC: 13880 AN: 41466

American (AMR) AF: 0.142 AC: 2165 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3466

East Asian (EAS) AF: 0.223 AC: 1151 AN: 5172

South Asian (SAS) AF: 0.220 AC: 1060 AN: 4824

European-Finnish (FIN) AF: 0.303 AC: 3199 AN: 10566

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15428 AN: 67980

Other (OTH) AF: 0.230 AC: 486 AN: 2114

Alfa AF: 0.232 Hom.: 17024

Bravo AF: 0.242

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.87
PhyloP100		0.0030
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6935269; hg19: chr6-32260350;