6-32371870-T-G

Variant names:

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

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.-164A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000174 in 573,068 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 0.0000017 (0 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: 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=-0.81).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	NM_001286474.2	MANE Select	c.-164A>C		5_prime_UTR	Exon 1 of 26	NP_001273403.1	A0A1U9X7D1
	TSBP1	NM_006781.5		c.-164A>C		5_prime_UTR	Exon 1 of 23	NP_006772.3
	TSBP1	NM_001286475.2		c.-164A>C		5_prime_UTR	Exon 1 of 24	NP_001273404.1	E9PLW3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	ENST00000533191.6	TSL:1 MANE Select	c.-164A>C		5_prime_UTR	Exon 1 of 26	ENSP00000431199.1	Q5SRN2-3
	TSBP1	ENST00000442822.6	TSL:1	c.-164A>C		5_prime_UTR	Exon 1 of 26	ENSP00000411164.2	C9J9T8
	TSBP1	ENST00000447241.6	TSL:5	c.-164A>C		5_prime_UTR	Exon 1 of 23	ENSP00000415517.2	Q5SRN2-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000174 AC: 1 AN: 573068 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 306924

African (AFR) AF: 0.00 AC: 0 AN: 16348

American (AMR) AF: 0.00 AC: 0 AN: 33046

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17490

East Asian (EAS) AF: 0.00 AC: 0 AN: 33236

South Asian (SAS) AF: 0.00 AC: 0 AN: 56768

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35146

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3976

European-Non Finnish (NFE) AF: 0.00000289 AC: 1 AN: 345948

Other (OTH) AF: 0.00 AC: 0 AN: 31110

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.77
PhyloP100		0.30
PromoterAI		-0.0056	Neutral

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;