rs7899305

Variant names:

• chr10-13157611-C-T
• rs7899305
• ENST00000447253.1:n.526G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BTBD7P1		n.13157611C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD7P1	ENST00000447253.1	n.526G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.282 AC: 3579 AN: 12682

American (AMR) AF: 0.440 AC: 10400 AN: 23618

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 4497 AN: 14090

East Asian (EAS) AF: 0.254 AC: 8340 AN: 32822

South Asian (SAS) AF: 0.250 AC: 11738 AN: 46878

European-Finnish (FIN) AF: 0.205 AC: 7611 AN: 37084

Middle Eastern (MID) AF: 0.391 AC: 1227 AN: 3142

European-Non Finnish (NFE) AF: 0.279 AC: 82778 AN: 296246

Other (OTH) AF: 0.302 AC: 8203 AN: 27182

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

African (AFR) AF: 0.288 AC: 11488 AN: 39954

American (AMR) AF: 0.412 AC: 6129 AN: 14890

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1091 AN: 3452

East Asian (EAS) AF: 0.334 AC: 1689 AN: 5058

South Asian (SAS) AF: 0.250 AC: 1185 AN: 4736

European-Finnish (FIN) AF: 0.200 AC: 2001 AN: 10016

Middle Eastern (MID) AF: 0.361 AC: 104 AN: 288

European-Non Finnish (NFE) AF: 0.282 AC: 19098 AN: 67696

Other (OTH) AF: 0.346 AC: 720 AN: 2082

Alfa AF: 0.296 Hom.: 26285

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
PhyloP100		0.47

Splicing

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

Other links and lift over

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