3-180575043-T-G

Position:

• chr3-180575043-T-G

Variant summary

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

The ENST00000472596.1(TTC14-DT):​n.420-8182A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,240 control chromosomes in the GnomAD database, including 432 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 0.073 (432 hom., cov: 32)
• Consequence: TTC14-DT ENST00000472596.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723

Genes affected

TTC14-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC14-DT	NR_183700.1	n.521+9305A>C		intron_variant
TTC14-DT	NR_183701.1	n.598-8182A>C		intron_variant
TTC14-DT	NR_183702.1	n.511-8182A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC14-DT	ENST00000472596.1	n.420-8182A>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11053 AN: 152122 Hom.: 433 Cov.: 32

Gnomad AFR AF: 0.0926

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0726 AC: 11057 AN: 152240 Hom.: 432 Cov.: 32 AF XY: 0.0713 AC XY: 5312 AN XY: 74466

Gnomad4 AFR AF: 0.0925

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.0553

Gnomad4 EAS AF: 0.00250

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0484

Gnomad4 NFE AF: 0.0678

Gnomad4 OTH AF: 0.0786

Alfa AF: 0.0228 Hom.: 15

Bravo AF: 0.0745

Asia WGS AF: 0.0680 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11708495; hg19: chr3-180292831;