3-180575043-T-G

Variant names:

• chr3-180575043-T-G
• rs11708495
• ENST00000472596.1:n.420-8182A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

TTC14-DT (HGNC:52912): (TTC14 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000472596.1. 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
	TTC14-DT	NR_183700.1		n.521+9305A>C		intron	N/A
	TTC14-DT	NR_183701.1		n.598-8182A>C		intron	N/A
	TTC14-DT	NR_183702.1		n.511-8182A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC14-DT	ENST00000472596.1	TSL:4	n.420-8182A>C		intron	N/A
	TTC14-DT	ENST00000830817.1		n.140-8182A>C		intron	N/A
	TTC14-DT	ENST00000830818.1		n.524+8457A>C		intron	N/A

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

African (AFR) AF: 0.0925 AC: 3843 AN: 41532

American (AMR) AF: 0.0674 AC: 1032 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0553 AC: 192 AN: 3470

East Asian (EAS) AF: 0.00250 AC: 13 AN: 5190

South Asian (SAS) AF: 0.115 AC: 553 AN: 4818

European-Finnish (FIN) AF: 0.0484 AC: 513 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0678 AC: 4608 AN: 68004

Other (OTH) AF: 0.0786 AC: 166 AN: 2112

Alfa AF: 0.0254 Hom.: 21

Bravo AF: 0.0745

Asia WGS AF: 0.0680 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.45
PhyloP100		0.72
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11708495; hg19: chr3-180292831;