chr3-180498066-A-G

Variant names:

• chr3-180498066-A-G
• rs9857056
• ENST00000830817.1:n.408-6205T>C

Variant summary

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

The ENST00000830817.1(TTC14-DT):​n.408-6205T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,954 control chromosomes in the GnomAD database, including 10,964 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 0.32 (10964 hom., cov: 32)
• Consequence: TTC14-DT ENST00000830817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 6 publications found

Genes affected

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

LINC02053 (HGNC:52893): (long intergenic non-protein coding RNA 2053)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830817.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC14-DT	NR_183700.1		n.522-16207T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC14-DT	ENST00000830817.1		n.408-6205T>C		intron	N/A
	TTC14-DT	ENST00000830818.1		n.658-6205T>C		intron	N/A
	TTC14-DT	ENST00000830819.1		n.416-6205T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49170 AN: 151836 Hom.: 10924 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.00425

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.324 AC: 49269 AN: 151954 Hom.: 10964 Cov.: 32 AF XY: 0.320 AC XY: 23734 AN XY: 74264

African (AFR) AF: 0.634 AC: 26254 AN: 41426

American (AMR) AF: 0.280 AC: 4275 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3468

East Asian (EAS) AF: 0.00426 AC: 22 AN: 5164

South Asian (SAS) AF: 0.204 AC: 984 AN: 4820

European-Finnish (FIN) AF: 0.184 AC: 1946 AN: 10576

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14103 AN: 67948

Other (OTH) AF: 0.311 AC: 652 AN: 2096

Alfa AF: 0.287 Hom.: 1123

Bravo AF: 0.344

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.62
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9857056; hg19: chr3-180215854;