rs7899305

Positions:

• chr10-13157611-C-T

Variant summary

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

The ENST00000447253.1(BTBD7P1):​n.526G>A 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 0.283 in 642,818 control chromosomes in the GnomAD database, including 27,645 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 0.29 (6628 hom., cov: 29)
  • Exomes 𝑓: 0.28 (21017 hom.)
• Consequence: BTBD7P1 ENST00000447253.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

Genes affected

BTBD7P1 (HGNC:44875): (BTB domain containing 7 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD7P1	ENST00000447253.1	n.526G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 43715 AN: 148968 Hom.: 6628 Cov.: 29

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.348

GnomAD4 exome AF: 0.280 AC: 138373 AN: 493744 Hom.: 21017 Cov.: 4 AF XY: 0.278 AC XY: 73344 AN XY: 263962

Gnomad4 AFR exome AF: 0.282

Gnomad4 AMR exome AF: 0.440

Gnomad4 ASJ exome AF: 0.319

Gnomad4 EAS exome AF: 0.254

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.205

Gnomad4 NFE exome AF: 0.279

Gnomad4 OTH exome AF: 0.302

GnomAD4 genome AF: 0.293 AC: 43731 AN: 149074 Hom.: 6628 Cov.: 29 AF XY: 0.293 AC XY: 21231 AN XY: 72574

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.346

Alfa AF: 0.298 Hom.: 11897

Bravo AF: 0.318

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	9.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7899305; hg19: chr10-13199611; COSMIC: COSV66388963;