ENST00000425494.1:n.1181A>G

Variant names:

• chr10-37530456-A-G
• rs7082044
• ENST00000425494.1:n.1181A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425494.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC1P1	ENST00000425494.1	TSL:6	n.1181A>G		non_coding_transcript_exon	Exon 3 of 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

African (AFR) AF: 0.200 AC: 3378 AN: 16876

American (AMR) AF: 0.112 AC: 2320 AN: 20710

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 2177 AN: 11438

East Asian (EAS) AF: 0.134 AC: 2134 AN: 15924

South Asian (SAS) AF: 0.142 AC: 7692 AN: 54134

European-Finnish (FIN) AF: 0.154 AC: 4668 AN: 30236

Middle Eastern (MID) AF: 0.236 AC: 838 AN: 3552

European-Non Finnish (NFE) AF: 0.235 AC: 164103 AN: 699760

Other (OTH) AF: 0.211 AC: 7199 AN: 34140

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

African (AFR) AF: 0.228 AC: 9287 AN: 40670

American (AMR) AF: 0.175 AC: 2665 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3472

East Asian (EAS) AF: 0.151 AC: 778 AN: 5154

South Asian (SAS) AF: 0.168 AC: 809 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1770 AN: 10604

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17471 AN: 67986

Other (OTH) AF: 0.238 AC: 501 AN: 2102

Alfa AF: 0.233 Hom.: 604

Bravo AF: 0.231

Asia WGS AF: 0.163 AC: 566 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	18
DANN	Benign	0.45
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs7082044; hg19: chr10-37819384;