rs12587630

Variant names:

• chr14-37597370-A-G
• rs12587630
• NM_001310135.5:c.-96+1362A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-37597370-A-G
• chr14-37597370-A-T

Variant summary

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

The NM_001310135.5(TTC6):​c.-96+1362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 152,108 control chromosomes in the GnomAD database, including 183 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 0.031 (183 hom., cov: 31)
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 3 publications found

Genes affected

TTC6 (HGNC:19739): (tetratricopeptide repeat domain 6)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC6	NM_001310135.5	c.-96+1362A>G		intron_variant	Intron 1 of 32	ENST00000553443.6	NP_001297064.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC6	ENST00000553443.6	c.-96+1362A>G		intron_variant	Intron 1 of 32	5	NM_001310135.5	ENSP00000451131.1

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4644 AN: 151990 Hom.: 178 Cov.: 31

Gnomad AFR AF: 0.00839

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.00664

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0245

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0307 AC: 4665 AN: 152108 Hom.: 183 Cov.: 31 AF XY: 0.0317 AC XY: 2358 AN XY: 74342

African (AFR) AF: 0.00836 AC: 347 AN: 41490

American (AMR) AF: 0.0857 AC: 1308 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00664 AC: 23 AN: 3466

East Asian (EAS) AF: 0.167 AC: 863 AN: 5162

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4814

European-Finnish (FIN) AF: 0.0273 AC: 289 AN: 10590

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0245 AC: 1665 AN: 68000

Other (OTH) AF: 0.0327 AC: 69 AN: 2112

Alfa AF: 0.0302 Hom.: 227

Bravo AF: 0.0364

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.53
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12587630; hg19: chr14-38066575;