6-32278050-C-T

Variant names:

• chr6-32278050-C-T
• rs3115553
• ENST00000611838.1:n.131+22636C>T

Variant summary

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

The ENST00000611838.1(TSBP1-AS1):​n.131+22636C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,090 control chromosomes in the GnomAD database, including 5,119 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 (5119 hom., cov: 32)
• Consequence: TSBP1-AS1 ENST00000611838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 36 publications found

Genes affected

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611838.1. 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-AS1	NR_136244.1		n.440+15241C>T		intron	N/A
	TSBP1-AS1	NR_136245.1		n.242+22636C>T		intron	N/A
	TSBP1-AS1	NR_136246.1		n.242+22636C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	ENST00000611838.1	TSL:2	n.131+22636C>T		intron	N/A
	TSBP1-AS1	ENST00000642577.1		n.108+15241C>T		intron	N/A
	TSBP1-AS1	ENST00000644884.2		n.64+22636C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37970 AN: 151972 Hom.: 5106 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.250 AC: 38017 AN: 152090 Hom.: 5119 Cov.: 32 AF XY: 0.249 AC XY: 18469 AN XY: 74320

African (AFR) AF: 0.335 AC: 13882 AN: 41490

American (AMR) AF: 0.142 AC: 2169 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1153 AN: 5176

South Asian (SAS) AF: 0.220 AC: 1062 AN: 4830

European-Finnish (FIN) AF: 0.303 AC: 3195 AN: 10544

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15423 AN: 67984

Other (OTH) AF: 0.231 AC: 486 AN: 2108

Alfa AF: 0.231 Hom.: 16739

Bravo AF: 0.242

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs3115553; hg19: chr6-32245827;