rs7082044

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-37530456-A-C
• chr10-37530456-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000425494.1(TACC1P1):​n.1181A>C 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 0.00000112 in 894,046 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000011 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC1P1	ENST00000425494.1	TSL:6	n.1181A>C		non_coding_transcript_exon	Exon 3 of 5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000112 AC: 1 AN: 894046 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 448612

African (AFR) AF: 0.00 AC: 0 AN: 17004

American (AMR) AF: 0.00 AC: 0 AN: 20814

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11526

East Asian (EAS) AF: 0.00 AC: 0 AN: 16006

South Asian (SAS) AF: 0.00 AC: 0 AN: 54546

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30374

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3574

European-Non Finnish (NFE) AF: 0.00000142 AC: 1 AN: 705742

Other (OTH) AF: 0.00 AC: 0 AN: 34460

GnomAD4 genome Cov.: 32

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7082044;

hg19: chr10-37819384;