rs2395117

Variant names:

• chr6-32283104-T-C
• rs2395117
• ENST00000611838.1:n.131+27690T>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+27690T>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 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 ENST00000611838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 3 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=-1.07).
• 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+20295T>C		intron	N/A
	TSBP1-AS1	NR_136245.1		n.242+27690T>C		intron	N/A
	TSBP1-AS1	NR_136246.1		n.242+27690T>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+27690T>C		intron	N/A
	TSBP1-AS1	ENST00000642577.1		n.108+20295T>C		intron	N/A
	TSBP1-AS1	ENST00000644884.2		n.64+27690T>C		intron	N/A

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

African (AFR) AF: 0.335 AC: 13876 AN: 41448

American (AMR) AF: 0.142 AC: 2173 AN: 15286

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

East Asian (EAS) AF: 0.222 AC: 1150 AN: 5174

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4820

European-Finnish (FIN) AF: 0.303 AC: 3203 AN: 10572

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

European-Non Finnish (NFE) AF: 0.227 AC: 15429 AN: 67992

Other (OTH) AF: 0.229 AC: 483 AN: 2110

Alfa AF: 0.253 Hom.: 656

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	-1.1
CADD	Benign	0.21
DANN	Benign	0.33
PhyloP100		-2.6

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: rs2395117;

hg19: chr6-32250881;