6-32382677-G-A

Position:

• chr6-32382677-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_136245.1(TSBP1-AS1):​n.302+16838G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 152,220 control chromosomes in the GnomAD database, including 64 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 0.024 (64 hom., cov: 31)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

Genes affected

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1	n.302+16838G>A		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.501-287G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-7537G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 3599 AN: 152102 Hom.: 65 Cov.: 31

Gnomad AFR AF: 0.00553

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.0580

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0236 AC: 3596 AN: 152220 Hom.: 64 Cov.: 31 AF XY: 0.0228 AC XY: 1695 AN XY: 74428

Gnomad4 AFR AF: 0.00551

Gnomad4 AMR AF: 0.0126

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.00849

Gnomad4 SAS AF: 0.0575

Gnomad4 FIN AF: 0.0125

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0299 Hom.: 51

Bravo AF: 0.0228

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28732201; hg19: chr6-32350454;