rs927340

Positions:

• chr6-3023484-G-A

Variant summary

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

The NR_033884.3(HTATSF1P2):​n.407C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 156,968 control chromosomes in the GnomAD database, including 7,751 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 0.27 (7646 hom., cov: 33)
  • Exomes 𝑓: 0.20 (105 hom.)
• Consequence: HTATSF1P2 NR_033884.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

HTATSF1P2 (HGNC:38586): (HIV-1 Tat specific factor 1 pseudogene 2)

(HGNC:):

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 = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTATSF1P2	NR_033884.3	n.407C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTATSF1P2	ENST00000604204.1	n.289C>T		non_coding_transcript_exon_variant	1/1
	ENST00000675225.1	n.13G>A		non_coding_transcript_exon_variant	1/2
	ENST00000676390.1	n.13G>A		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41572 AN: 152046 Hom.: 7631 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.198 AC: 951 AN: 4804 Hom.: 105 Cov.: 0 AF XY: 0.191 AC XY: 533 AN XY: 2786

Gnomad4 AFR exome AF: 0.594

Gnomad4 AMR exome AF: 0.331

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.332

Gnomad4 SAS exome AF: 0.194

Gnomad4 FIN exome AF: 0.145

Gnomad4 NFE exome AF: 0.166

Gnomad4 OTH exome AF: 0.166

GnomAD4 genome AF: 0.274 AC: 41633 AN: 152164 Hom.: 7646 Cov.: 33 AF XY: 0.270 AC XY: 20083 AN XY: 74396

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.238

Alfa AF: 0.207 Hom.: 2736

Bravo AF: 0.298

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs927340; hg19: chr6-3023718;