rs2395117

chr6-32283104-T-C

Variant summary

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

The NR_136245.1(TSBP1-AS1):n.242+27690T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,080 control chromosomes in the GnomAD database, including 5,130 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 0.25 (5130 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

Genes affected

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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.242+27690T>C		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.440+20295T>C		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136246.1	n.242+27690T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.87+27690T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37972 AN: 151962 Hom.: 5117 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.250 AC: 38019 AN: 152080 Hom.: 5130 Cov.: 32 AF XY: 0.249 AC XY: 18484 AN XY: 74342

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.229

Alfa AF: 0.250 Hom.: 608

Bravo AF: 0.242

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.21
Dann	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2395117; hg19: chr6-32250881;