rs1265758

Variant names:

• chr6-32355752-A-C
• rs1265758
• NM_001286474.2:c.218-83T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32355752-A-C
• chr6-32355752-A-G
• chr6-32355752-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001286474.2(TSBP1):​c.218-83T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 36 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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.218-83T>G		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.218-83T>G		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.197-83T>G		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.218-83T>G		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.197-83T>G		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.218-83T>G		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1312280 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 648314

African (AFR) AF: 0.00 AC: 0 AN: 27496

American (AMR) AF: 0.00 AC: 0 AN: 25250

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22388

East Asian (EAS) AF: 0.00 AC: 0 AN: 34212

South Asian (SAS) AF: 0.00 AC: 0 AN: 68032

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35162

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5222

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1040190

Other (OTH) AF: 0.00 AC: 0 AN: 54328

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.17
DANN	Benign	0.39
PhyloP100		-0.93

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: rs1265758; hg19: chr6-32323529;