rs7082044

Positions:

• chr10-37530456-A-G

Variant summary

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

The ENST00000425494.1(TACC1P1):​n.1181A>G 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 0.221 in 1,038,012 control chromosomes in the GnomAD database, including 26,965 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 0.23 (4543 hom., cov: 32)
  • Exomes 𝑓: 0.22 (22422 hom.)
• Consequence: TACC1P1 ENST00000425494.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.92

Genes affected

TACC1P1 (HGNC:44974): (transforming acidic coiled-coil containing protein 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 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
TACC1P1	ENST00000425494.1	n.1181A>G		non_coding_transcript_exon_variant	3/5

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34356 AN: 151126 Hom.: 4517 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.240

GnomAD4 exome AF: 0.219 AC: 194509 AN: 886770 Hom.: 22422 Cov.: 13 AF XY: 0.217 AC XY: 96387 AN XY: 444810

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.112

Gnomad4 ASJ exome AF: 0.190

Gnomad4 EAS exome AF: 0.134

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.154

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.211

GnomAD4 genome AF: 0.228 AC: 34438 AN: 151242 Hom.: 4543 Cov.: 32 AF XY: 0.221 AC XY: 16324 AN XY: 73950

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.238

Alfa AF: 0.234 Hom.: 584

Bravo AF: 0.231

Asia WGS AF: 0.163 AC: 566 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	18
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: rs7082044; hg19: chr10-37819384;