chr10-37523542-G-C

Variant names:

• chr10-37523542-G-C
• rs11011224
• ENST00000425494.1:n.532G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425494.1(TACC1P1):​n.532G>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 0.162 in 680,482 control chromosomes in the GnomAD database, including 9,618 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 0.17 (2359 hom., cov: 32)
  • Exomes 𝑓: 0.16 (7259 hom.)
• Consequence: TACC1P1 ENST00000425494.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC1P1		n.37523542G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACC1P1	ENST00000425494.1	n.532G>C		non_coding_transcript_exon_variant	Exon 1 of 5	6

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25519 AN: 152008 Hom.: 2335 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.160 AC: 84788 AN: 528354 Hom.: 7259 Cov.: 5 AF XY: 0.160 AC XY: 46184 AN XY: 288452

African (AFR) AF: 0.230 AC: 3364 AN: 14638

American (AMR) AF: 0.100 AC: 3772 AN: 37722

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 2095 AN: 15842

East Asian (EAS) AF: 0.150 AC: 3161 AN: 21138

South Asian (SAS) AF: 0.149 AC: 10014 AN: 67294

European-Finnish (FIN) AF: 0.101 AC: 3056 AN: 30126

Middle Eastern (MID) AF: 0.161 AC: 554 AN: 3448

European-Non Finnish (NFE) AF: 0.175 AC: 54649 AN: 312214

Other (OTH) AF: 0.159 AC: 4123 AN: 25932

GnomAD4 genome AF: 0.168 AC: 25589 AN: 152128 Hom.: 2359 Cov.: 32 AF XY: 0.166 AC XY: 12326 AN XY: 74382

African (AFR) AF: 0.221 AC: 9157 AN: 41490

American (AMR) AF: 0.120 AC: 1834 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3468

East Asian (EAS) AF: 0.153 AC: 792 AN: 5170

South Asian (SAS) AF: 0.150 AC: 724 AN: 4816

European-Finnish (FIN) AF: 0.105 AC: 1111 AN: 10604

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10926 AN: 67980

Other (OTH) AF: 0.161 AC: 340 AN: 2108

Alfa AF: 0.157 Hom.: 247

Bravo AF: 0.172

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.72
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11011224; hg19: chr10-37812470;