chr6-32377506-C-A

Position:

• chr6-32377506-C-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+11667C>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 0.0415 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_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.302+11667C>A		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.501-5458C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-12708C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0565

Gnomad4 AMR AF: 0.0543

Gnomad4 ASJ AF: 0.00606

Gnomad4 EAS AF: 0.0269

Gnomad4 SAS AF: 0.0486

Gnomad4 FIN AF: 0.0657

Gnomad4 NFE AF: 0.0284

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0253 Hom.: 83

Bravo AF: 0.0414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7758128; hg19: chr6-32345283;