rs2278528

Positions:

• chr2-19902071-C-G
• chr2-19902071-C-T

Variant summary

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

The ENST00000607190.2(TTC32-DT):​n.50C>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 0.208 in 515,250 control chromosomes in the GnomAD database, including 13,202 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 0.20 (3384 hom., cov: 33)
  • Exomes 𝑓: 0.21 (9818 hom.)
• Consequence: TTC32-DT ENST00000607190.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

TTC32-DT (HGNC:55236): (TTC32 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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
TTC32-DT	ENST00000607190.2	n.50C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30544 AN: 152024 Hom.: 3379 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.211 AC: 76578 AN: 363108 Hom.: 9818 Cov.: 5 AF XY: 0.221 AC XY: 41770 AN XY: 189342

Gnomad4 AFR exome AF: 0.210

Gnomad4 AMR exome AF: 0.220

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.448

Gnomad4 SAS exome AF: 0.391

Gnomad4 FIN exome AF: 0.161

Gnomad4 NFE exome AF: 0.168

Gnomad4 OTH exome AF: 0.202

GnomAD4 genome AF: 0.201 AC: 30586 AN: 152142 Hom.: 3384 Cov.: 33 AF XY: 0.206 AC XY: 15347 AN XY: 74378

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.216

Alfa AF: 0.0775 Hom.: 94

Bravo AF: 0.201

Asia WGS AF: 0.411 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.93
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278528; hg19: chr2-20101832;