rs10997795

Positions:

• chr10-67751147-C-T

Variant summary

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

The ENST00000425765.1(AKR1B10P1):​n.864C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.119 in 1,306,556 control chromosomes in the GnomAD database, including 14,928 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 0.18 (3437 hom., cov: 32)
  • Exomes 𝑓: 0.11 (11491 hom.)
• Consequence: AKR1B10P1 ENST00000425765.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.95

Genes affected

AKR1B10P1 (HGNC:45062): (aldo-keto reductase family 1 member B10 pseudogene 1)

CTNNA3 (HGNC:2511): (catenin alpha 3) This gene encodes a protein that belongs to the vinculin/alpha-catenin family. The encoded protein plays a role in cell-cell adhesion in muscle cells. Mutations in this gene are associated with arrhythmogenic right ventricular dysplasia, familial 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTNNA3	XM_047425124.1	c.-47+12287G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKR1B10P1	ENST00000425765.1	n.864C>T		non_coding_transcript_exon_variant	1/1
CTNNA3	ENST00000684154.1	c.-2+12287G>A		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26754 AN: 152068 Hom.: 3422 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.112 AC: 129231 AN: 1154368 Hom.: 11491 Cov.: 23 AF XY: 0.114 AC XY: 66891 AN XY: 587952

Gnomad4 AFR exome AF: 0.346

Gnomad4 AMR exome AF: 0.148

Gnomad4 ASJ exome AF: 0.0858

Gnomad4 EAS exome AF: 0.445

Gnomad4 SAS exome AF: 0.201

Gnomad4 FIN exome AF: 0.146

Gnomad4 NFE exome AF: 0.0755

Gnomad4 OTH exome AF: 0.133

GnomAD4 genome AF: 0.176 AC: 26815 AN: 152188 Hom.: 3437 Cov.: 32 AF XY: 0.181 AC XY: 13466 AN XY: 74404

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.0752

Gnomad4 OTH AF: 0.167

Alfa AF: 0.119 Hom.: 278

Bravo AF: 0.187

Asia WGS AF: 0.310 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10997795; hg19: chr10-69510905;