2-19902071-C-G

Variant names:

• chr2-19902071-C-G
• rs2278528
• ENST00000607190.3:n.739C>G

Variant summary

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

The ENST00000607190.3(TTC32-DT):​n.739C>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 ENST00000607190.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 8 publications found

Genes affected

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

TTC32 (HGNC:32954): (tetratricopeptide repeat domain 32)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607190.3. 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
	TTC32	NM_001008237.3	MANE Select	c.-217G>C		upstream_gene	N/A	NP_001008238.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC32-DT	ENST00000607190.3	TSL:6	n.739C>G		non_coding_transcript_exon	Exon 1 of 1
	TTC32-DT	ENST00000731642.1		n.394-32C>G		intron	N/A
	TTC32-DT	ENST00000731643.1		n.134-32C>G		intron	N/A

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

African (AFR) AF: 0.210 AC: 1987 AN: 9478

American (AMR) AF: 0.220 AC: 2534 AN: 11502

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 1776 AN: 11420

East Asian (EAS) AF: 0.448 AC: 10761 AN: 24024

South Asian (SAS) AF: 0.391 AC: 12501 AN: 31932

European-Finnish (FIN) AF: 0.161 AC: 4077 AN: 25344

Middle Eastern (MID) AF: 0.301 AC: 498 AN: 1656

European-Non Finnish (NFE) AF: 0.168 AC: 38103 AN: 226226

Other (OTH) AF: 0.202 AC: 4341 AN: 21526

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

African (AFR) AF: 0.210 AC: 8733 AN: 41492

American (AMR) AF: 0.236 AC: 3607 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2131 AN: 5178

South Asian (SAS) AF: 0.379 AC: 1828 AN: 4820

European-Finnish (FIN) AF: 0.161 AC: 1704 AN: 10598

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11365 AN: 67982

Other (OTH) AF: 0.216 AC: 456 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.93
DANN	Benign	0.41
PhyloP100		-0.34
PromoterAI		0.054	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2278528; hg19: chr2-20101832;