rs688011

Positions:

• chr11-113283448-G-A

Variant summary

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

The ENST00000526487.6(TTC12-DT):​n.154-2816C>T variant causes a intron, non coding transcript 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 ENST00000526487.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412

Genes affected

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

LOC124902814 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902814	XR_007062991.1	n.128-2816C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC12-DT	ENST00000526487.6	n.154-2816C>T		intron_variant, non_coding_transcript_variant		3
TTC12-DT	ENST00000529416.5	n.134+409C>T		intron_variant, non_coding_transcript_variant		3
TTC12-DT	ENST00000533504.3	n.147-2816C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.0959

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.260

Alfa AF: 0.276 Hom.: 1110

Bravo AF: 0.251

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs688011; hg19: chr11-113154170;