rs3130320

Variant names:

• chr6-32255481-T-C
• rs3130320
• ENST00000611838.1:n.131+67T>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+67T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 154,388 control chromosomes in the GnomAD database, including 36,478 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 0.68 (35791 hom., cov: 32)
  • Exomes 𝑓: 0.76 (687 hom.)
• Consequence: TSBP1-AS1 ENST00000611838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 70 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.767 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.242+67T>C		intron	N/A
	TSBP1-AS1	NR_136245.1		n.242+67T>C		intron	N/A
	TSBP1-AS1	NR_136246.1		n.242+67T>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+67T>C		intron	N/A
	TSBP1-AS1	ENST00000644884.2		n.64+67T>C		intron	N/A
	TSBP1-AS1	ENST00000645134.1		n.87+67T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103716 AN: 151968 Hom.: 35759 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.715

GnomAD4 exome AF: 0.762 AC: 1753 AN: 2302 Hom.: 687 Cov.: 0 AF XY: 0.780 AC XY: 1012 AN XY: 1298

African (AFR) AF: 0.944 AC: 17 AN: 18

American (AMR) AF: 0.868 AC: 66 AN: 76

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 42 AN: 48

East Asian (EAS) AF: 0.967 AC: 29 AN: 30

South Asian (SAS) AF: 0.896 AC: 346 AN: 386

European-Finnish (FIN) AF: 0.627 AC: 74 AN: 118

Middle Eastern (MID) AF: 0.833 AC: 5 AN: 6

European-Non Finnish (NFE) AF: 0.720 AC: 1076 AN: 1494

Other (OTH) AF: 0.778 AC: 98 AN: 126

GnomAD4 genome AF: 0.683 AC: 103804 AN: 152086 Hom.: 35791 Cov.: 32 AF XY: 0.683 AC XY: 50790 AN XY: 74328

African (AFR) AF: 0.711 AC: 29512 AN: 41504

American (AMR) AF: 0.779 AC: 11899 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2974 AN: 3468

East Asian (EAS) AF: 0.773 AC: 3992 AN: 5166

South Asian (SAS) AF: 0.759 AC: 3658 AN: 4818

European-Finnish (FIN) AF: 0.574 AC: 6068 AN: 10574

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43341 AN: 67962

Other (OTH) AF: 0.714 AC: 1511 AN: 2116

Alfa AF: 0.660 Hom.: 116347

Bravo AF: 0.699

Asia WGS AF: 0.746 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.78
PhyloP100		-0.031

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: rs3130320;

hg19: chr6-32223258;