NM_001286474.2:c.*199T>C

Variant names:

• chr6-32292782-A-G
• rs482194
• NM_001286474.2:c.*199T>C

Variant summary

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

The NM_001286474.2(TSBP1):​c.*199T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 535,074 control chromosomes in the GnomAD database, including 41,925 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 0.33 (9627 hom., cov: 32)
  • Exomes 𝑓: 0.40 (32298 hom.)
• Consequence: TSBP1 NM_001286474.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 20 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 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.*199T>C		3_prime_UTR	Exon 26 of 26	NP_001273403.1
	TSBP1	NM_006781.5		c.*199T>C		3_prime_UTR	Exon 23 of 23	NP_006772.3
	TSBP1	NM_001286475.2		c.*199T>C		3_prime_UTR	Exon 24 of 24	NP_001273404.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	ENST00000533191.6	TSL:1 MANE Select	c.*199T>C		3_prime_UTR	Exon 26 of 26	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.1359+505T>C		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.*199T>C		3_prime_UTR	Exon 23 of 23	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50863 AN: 152010 Hom.: 9615 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.356

GnomAD4 exome AF: 0.400 AC: 153327 AN: 382946 Hom.: 32298 Cov.: 3 AF XY: 0.406 AC XY: 81412 AN XY: 200590

African (AFR) AF: 0.152 AC: 1477 AN: 9712

American (AMR) AF: 0.488 AC: 5798 AN: 11874

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 6838 AN: 12202

East Asian (EAS) AF: 0.309 AC: 8542 AN: 27640

South Asian (SAS) AF: 0.461 AC: 13341 AN: 28948

European-Finnish (FIN) AF: 0.309 AC: 8686 AN: 28122

Middle Eastern (MID) AF: 0.560 AC: 995 AN: 1776

European-Non Finnish (NFE) AF: 0.412 AC: 98689 AN: 239768

Other (OTH) AF: 0.391 AC: 8961 AN: 22904

GnomAD4 genome AF: 0.335 AC: 50891 AN: 152128 Hom.: 9627 Cov.: 32 AF XY: 0.335 AC XY: 24887 AN XY: 74366

African (AFR) AF: 0.160 AC: 6662 AN: 41522

American (AMR) AF: 0.446 AC: 6800 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1966 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1891 AN: 5174

South Asian (SAS) AF: 0.428 AC: 2066 AN: 4828

European-Finnish (FIN) AF: 0.297 AC: 3143 AN: 10596

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27119 AN: 67958

Other (OTH) AF: 0.352 AC: 744 AN: 2112

Alfa AF: 0.383 Hom.: 23757

Bravo AF: 0.340

Asia WGS AF: 0.343 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.65
PhyloP100		1.2
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: rs482194; hg19: chr6-32260559;