rs544358

Variant names:

• chr6-32305381-G-C
• rs544358
• NM_001286474.2:c.575-2752C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32305381-G-C
• chr6-32305381-G-T

Variant summary

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

The NM_001286474.2(TSBP1):​c.575-2752C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,048 control chromosomes in the GnomAD database, including 9,622 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 (9622 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 16 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.575-2752C>G		intron_variant	Intron 22 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.575-2752C>G		intron_variant	Intron 22 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50864 AN: 151930 Hom.: 9610 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.335 AC: 50892 AN: 152048 Hom.: 9622 Cov.: 32 AF XY: 0.335 AC XY: 24907 AN XY: 74336

African (AFR) AF: 0.161 AC: 6671 AN: 41494

American (AMR) AF: 0.445 AC: 6808 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1899 AN: 5178

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4816

European-Finnish (FIN) AF: 0.297 AC: 3136 AN: 10546

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

European-Non Finnish (NFE) AF: 0.399 AC: 27112 AN: 67950

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.245 Hom.: 627

Bravo AF: 0.340

Asia WGS AF: 0.343 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.62
PhyloP100		0.36
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: rs544358; hg19: chr6-32273158;