rs2050189

Variant names:

• chr6-32371870-T-C
• rs2050189
• NM_001286474.2:c.-164A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32371870-T-C
• chr6-32371870-T-G

Variant summary

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

The NM_001286474.2(TSBP1):​c.-164A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 724,760 control chromosomes in the GnomAD database, including 21,496 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 0.19 (3371 hom., cov: 32)
  • Exomes 𝑓: 0.24 (18125 hom.)
• Consequence: TSBP1 NM_001286474.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 40 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.-164A>G		5_prime_UTR_variant	Exon 1 of 26	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.-164A>G		5_prime_UTR_variant	Exon 1 of 26	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28819 AN: 152092 Hom.: 3348 Cov.: 32

Gnomad AFR AF: 0.0716

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.205

GnomAD4 exome AF: 0.239 AC: 136573 AN: 572550 Hom.: 18125 Cov.: 7 AF XY: 0.244 AC XY: 74934 AN XY: 306674

African (AFR) AF: 0.0737 AC: 1204 AN: 16342

American (AMR) AF: 0.345 AC: 11386 AN: 32998

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 2789 AN: 17486

East Asian (EAS) AF: 0.341 AC: 11337 AN: 33204

South Asian (SAS) AF: 0.350 AC: 19828 AN: 56706

European-Finnish (FIN) AF: 0.202 AC: 7093 AN: 35128

Middle Eastern (MID) AF: 0.261 AC: 1035 AN: 3972

European-Non Finnish (NFE) AF: 0.216 AC: 74676 AN: 345640

Other (OTH) AF: 0.233 AC: 7225 AN: 31074

GnomAD4 genome AF: 0.190 AC: 28867 AN: 152210 Hom.: 3371 Cov.: 32 AF XY: 0.193 AC XY: 14374 AN XY: 74434

African (AFR) AF: 0.0720 AC: 2989 AN: 41540

American (AMR) AF: 0.277 AC: 4240 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3472

East Asian (EAS) AF: 0.354 AC: 1832 AN: 5174

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4820

European-Finnish (FIN) AF: 0.199 AC: 2112 AN: 10590

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14821 AN: 67992

Other (OTH) AF: 0.211 AC: 446 AN: 2114

Alfa AF: 0.220 Hom.: 16155

Bravo AF: 0.188

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.78
PhyloP100		0.30
PromoterAI		0.0077	Neutral
Mutation Taster		=300/0	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: rs2050189; hg19: chr6-32339647; COSMIC: COSV66658378;