ENST00000526487.6:n.153+4850G>A

Variant names:

• chr11-113309480-C-T
• rs4517559
• ENST00000526487.6:n.153+4850G>A

Variant summary

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

The ENST00000526487.6(TTC12-DT):​n.153+4850G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,060 control chromosomes in the GnomAD database, including 26,306 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 0.58 (26306 hom., cov: 33)
• Consequence: TTC12-DT ENST00000526487.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 9 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC12-DT	NR_186360.1	n.127+4850G>A		intron_variant	Intron 1 of 3
TTC12-DT	NR_186361.1	n.127+4850G>A		intron_variant	Intron 1 of 4
TTC12-DT	NR_199707.1	n.127+4850G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC12-DT	ENST00000526487.6	n.153+4850G>A		intron_variant	Intron 1 of 3	3
TTC12-DT	ENST00000533504.3	n.146+4850G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88712 AN: 151942 Hom.: 26297 Cov.: 33

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.584 AC: 88759 AN: 152060 Hom.: 26306 Cov.: 33 AF XY: 0.580 AC XY: 43100 AN XY: 74322

African (AFR) AF: 0.524 AC: 21717 AN: 41444

American (AMR) AF: 0.581 AC: 8881 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2152 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2486 AN: 5156

South Asian (SAS) AF: 0.610 AC: 2943 AN: 4828

European-Finnish (FIN) AF: 0.539 AC: 5685 AN: 10548

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.632 AC: 42971 AN: 68004

Other (OTH) AF: 0.589 AC: 1246 AN: 2114

Alfa AF: 0.620 Hom.: 46284

Bravo AF: 0.583

Asia WGS AF: 0.575 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs4517559; hg19: chr11-113180202;