rs4938006

Variant names:

• chr11-113289725-A-G
• rs4938006
• ENST00000526487.6:n.154-9093T>C

Variant summary

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

The ENST00000533504.3(TTC12-DT):​n.147-9093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,244 control chromosomes in the GnomAD database, including 1,137 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 0.12 (1137 hom., cov: 33)
• Consequence: TTC12-DT ENST00000533504.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533504.3. 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_186360.1		n.128-9093T>C		intron	N/A
	TTC12-DT	NR_186361.1		n.128-5135T>C		intron	N/A
	TTC12-DT	NR_199707.1		n.128-5135T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC12-DT	ENST00000526487.6	TSL:3	n.154-9093T>C		intron	N/A
	TTC12-DT	ENST00000533504.3	TSL:2	n.147-9093T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17593 AN: 152124 Hom.: 1135 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00617

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.116 AC: 17617 AN: 152244 Hom.: 1137 Cov.: 33 AF XY: 0.118 AC XY: 8794 AN XY: 74442

African (AFR) AF: 0.130 AC: 5381 AN: 41530

American (AMR) AF: 0.0658 AC: 1007 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3468

East Asian (EAS) AF: 0.00619 AC: 32 AN: 5172

South Asian (SAS) AF: 0.173 AC: 834 AN: 4828

European-Finnish (FIN) AF: 0.178 AC: 1889 AN: 10612

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7699 AN: 68008

Other (OTH) AF: 0.107 AC: 225 AN: 2110

Alfa AF: 0.110 Hom.: 685

Bravo AF: 0.107

Asia WGS AF: 0.101 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.75
PhyloP100		-0.54

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4938006;

hg19: chr11-113160447;