rs7758128

Variant names:

• chr6-32377506-C-A
• rs7758128
• ENST00000642577.1:n.168+11667C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32377506-C-A
• chr6-32377506-C-T

Variant summary

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

The NR_136244.1(TSBP1-AS1):​n.501-5458C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 152,102 control chromosomes in the GnomAD database, including 145 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 0.041 (145 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 19 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_136244.1. 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.501-5458C>A		intron	N/A
	TSBP1-AS1	NR_136245.1		n.302+11667C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	ENST00000642577.1		n.168+11667C>A		intron	N/A
	TSBP1-AS1	ENST00000644884.2		n.125-9475C>A		intron	N/A
	TSBP1-AS1	ENST00000645134.1		n.88-12708C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6303 AN: 151984 Hom.: 145 Cov.: 32

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0284

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0415 AC: 6306 AN: 152102 Hom.: 145 Cov.: 32 AF XY: 0.0427 AC XY: 3175 AN XY: 74338

African (AFR) AF: 0.0565 AC: 2344 AN: 41498

American (AMR) AF: 0.0543 AC: 830 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3468

East Asian (EAS) AF: 0.0269 AC: 139 AN: 5172

South Asian (SAS) AF: 0.0486 AC: 234 AN: 4810

European-Finnish (FIN) AF: 0.0657 AC: 695 AN: 10582

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0284 AC: 1928 AN: 67980

Other (OTH) AF: 0.0464 AC: 98 AN: 2110

Alfa AF: 0.0314 Hom.: 337

Bravo AF: 0.0414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs7758128; hg19: chr6-32345283;