2-19902071-C-T

Variant names:

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

Variant summary

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

The ENST00000607190.3(TTC32-DT):​n.739C>T 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 0.00000582 in 515,758 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: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000055 (0 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: 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=-0.79).

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>A		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>T		non_coding_transcript_exon	Exon 1 of 1
	TTC32-DT	ENST00000731642.1		n.394-32C>T		intron	N/A
	TTC32-DT	ENST00000731643.1		n.134-32C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 152076 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000550 AC: 2 AN: 363682 Hom.: 0 Cov.: 5 AF XY: 0.00000527 AC XY: 1 AN XY: 189652

African (AFR) AF: 0.00 AC: 0 AN: 9498

American (AMR) AF: 0.00 AC: 0 AN: 11522

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11436

East Asian (EAS) AF: 0.00 AC: 0 AN: 24094

South Asian (SAS) AF: 0.00 AC: 0 AN: 31988

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25392

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1656

European-Non Finnish (NFE) AF: 0.00000883 AC: 2 AN: 226552

Other (OTH) AF: 0.00 AC: 0 AN: 21544

GnomAD4 genome AF: 0.00000658 AC: 1 AN: 152076 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74282

African (AFR) AF: 0.00 AC: 0 AN: 41388

American (AMR) AF: 0.00 AC: 0 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68004

Other (OTH) AF: 0.00 AC: 0 AN: 2088

Alfa AF: 0.00 Hom.: 94

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.86
PhyloP100		-0.34
PromoterAI		-0.044	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;