rs4517559

Positions:

• chr11-113309480-C-T

Variant summary

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

The ENST00000526487.6(TTC12-DT):​n.153+4850G>A 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 0.584 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

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=-0.98).
• 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/exons	MANE	UniProt
LOC124902814	XR_007062991.1	n.127+4850G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC12-DT	ENST00000526487.6	n.153+4850G>A		intron_variant, non_coding_transcript_variant		3
TTC12-DT	ENST00000533504.3	n.146+4850G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.589

Alfa AF: 0.624 Hom.: 35065

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4517559; hg19: chr11-113180202;