rs6910071

Variant names:

• chr6-32315077-A-G
• rs6910071
• NM_001286474.2:c.574+695T>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.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
• Publications: 97 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=-0.9).
• 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 rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.574+695T>C		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.574+695T>C		intron_variant	Intron 22 of 25	1	NM_001286474.2	ENSP00000431199.1

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

African (AFR) AF: 0.0575 AC: 2389 AN: 41544

American (AMR) AF: 0.187 AC: 2858 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3472

East Asian (EAS) AF: 0.0703 AC: 364 AN: 5180

South Asian (SAS) AF: 0.0694 AC: 335 AN: 4824

European-Finnish (FIN) AF: 0.161 AC: 1708 AN: 10602

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13694 AN: 68006

Other (OTH) AF: 0.112 AC: 237 AN: 2114

Alfa AF: 0.183 Hom.: 12536

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
PhyloP100		0.043
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: rs6910071; hg19: chr6-32282854;