rs6910071

Positions:

• chr6-32315077-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286474.2(TSBP1):​c.574+695T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,250 control chromosomes in the GnomAD database, including 1,979 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 0.14 (1979 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.574+695T>C		intron_variant		ENST00000533191.6	NP_001273403.1
TSBP1-AS1	NR_136245.1	n.243-50703A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.574+695T>C		intron_variant		1	NM_001286474.2	ENSP00000431199	A2
TSBP1-AS1	ENST00000645134.1	n.87+59663A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21941 AN: 152132 Hom.: 1980 Cov.: 32

Gnomad AFR AF: 0.0576

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.0688

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.114

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 21952 AN: 152250 Hom.: 1979 Cov.: 32 AF XY: 0.141 AC XY: 10506 AN XY: 74440

Gnomad4 AFR AF: 0.0575

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.0703

Gnomad4 SAS AF: 0.0694

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.112

Alfa AF: 0.182 Hom.: 5102

Bravo AF: 0.146

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.27

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

Publications

LitVar

Other links and lift over

dbSNP: rs6910071; hg19: chr6-32282854;