rs140709

Variant names:

• chr6-12213177-CATT-C
• rs140709
• ENST00000789282.1:n.116-28870_116-28868delAAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000789282.1(ENSG00000302734):​n.116-28870_116-28868delAAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (8730 hom., cov: 0)
• Consequence: ENSG00000302734 ENST00000789282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839
• Publications: 2 publications found

Genes affected

ENSG00000302734 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789282.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302734	ENST00000789282.1		n.116-28870_116-28868delAAT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47123 AN: 151256 Hom.: 8730 Cov.: 0

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.311 AC: 47131 AN: 151366 Hom.: 8730 Cov.: 0 AF XY: 0.315 AC XY: 23270 AN XY: 73902

African (AFR) AF: 0.0961 AC: 3967 AN: 41270

American (AMR) AF: 0.430 AC: 6542 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1093 AN: 3460

East Asian (EAS) AF: 0.271 AC: 1395 AN: 5144

South Asian (SAS) AF: 0.435 AC: 2086 AN: 4800

European-Finnish (FIN) AF: 0.435 AC: 4499 AN: 10344

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26516 AN: 67832

Other (OTH) AF: 0.285 AC: 600 AN: 2108

Alfa AF: 0.332 Hom.: 911

Asia WGS AF: 0.323 AC: 1123 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.84

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: rs140709;

hg19: chr6-12213410;