rs688011

Variant names:

• chr11-113283448-G-A
• rs688011
• NR_199709.1:n.1270C>T

Variant summary

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

The NR_199709.1(TTC12-DT):​n.1270C>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 0.271 in 152,098 control chromosomes in the GnomAD database, including 5,920 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 0.27 (5920 hom., cov: 33)
• Consequence: TTC12-DT NR_199709.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 6 publications found

Genes affected

TTC12-DT (HGNC:55508): (TTC12 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_199709.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC12-DT	NR_199709.1		n.1270C>T		non_coding_transcript_exon	Exon 2 of 5
	TTC12-DT	NR_186360.1		n.128-2816C>T		intron	N/A
	TTC12-DT	NR_186361.1		n.861+409C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC12-DT	ENST00000526487.6	TSL:3	n.154-2816C>T		intron	N/A
	TTC12-DT	ENST00000529416.5	TSL:3	n.134+409C>T		intron	N/A
	TTC12-DT	ENST00000533504.3	TSL:2	n.147-2816C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41137 AN: 151980 Hom.: 5911 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.259

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.271 AC: 41166 AN: 152098 Hom.: 5920 Cov.: 33 AF XY: 0.274 AC XY: 20343 AN XY: 74362

African (AFR) AF: 0.234 AC: 9701 AN: 41504

American (AMR) AF: 0.192 AC: 2929 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3466

East Asian (EAS) AF: 0.0959 AC: 496 AN: 5170

South Asian (SAS) AF: 0.418 AC: 2011 AN: 4814

European-Finnish (FIN) AF: 0.343 AC: 3632 AN: 10574

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20368 AN: 67968

Other (OTH) AF: 0.260 AC: 550 AN: 2114

Alfa AF: 0.276 Hom.: 1137

Bravo AF: 0.251

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.79
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs688011; hg19: chr11-113154170;