rs3130340

Variant names:

• chr6-32276850-T-C
• rs3130340
• ENST00000611838.1:n.131+21436T>C

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+21436T>C 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 151,834 control chromosomes in the GnomAD database, including 5,104 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 (5104 hom., cov: 29)
• Consequence: TSBP1-AS1 ENST00000611838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 66 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=-0.99).
• 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+14041T>C		intron	N/A
	TSBP1-AS1	NR_136245.1		n.242+21436T>C		intron	N/A
	TSBP1-AS1	NR_136246.1		n.242+21436T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	ENST00000611838.1	TSL:2	n.131+21436T>C		intron	N/A
	TSBP1-AS1	ENST00000642577.1		n.108+14041T>C		intron	N/A
	TSBP1-AS1	ENST00000644884.2		n.64+21436T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37864 AN: 151716 Hom.: 5092 Cov.: 29

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.302

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: 37910 AN: 151834 Hom.: 5104 Cov.: 29 AF XY: 0.248 AC XY: 18424 AN XY: 74210

African (AFR) AF: 0.334 AC: 13826 AN: 41352

American (AMR) AF: 0.142 AC: 2164 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1145 AN: 5160

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4818

European-Finnish (FIN) AF: 0.302 AC: 3179 AN: 10536

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

European-Non Finnish (NFE) AF: 0.227 AC: 15411 AN: 67932

Other (OTH) AF: 0.229 AC: 482 AN: 2104

Alfa AF: 0.232 Hom.: 17010

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	-0.99
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3130340;

hg19: chr6-32244627;