rs140759

Variant names:

• chr6-120068309-CAAAG-C
• rs140759
• ENST00000834274.1:n.95-60257_95-60254delAAAG

Variant summary

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

The ENST00000834274.1(ENSG00000308468):​n.95-60257_95-60254delAAAG 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 (7740 hom., cov: 0)
• Consequence: ENSG00000308468 ENST00000834274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 2 publications found

Genes affected

ENSG00000308468 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834274.1. 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
	ENSG00000308468	ENST00000834274.1		n.95-60257_95-60254delAAAG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47350 AN: 150794 Hom.: 7734 Cov.: 0

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.314 AC: 47365 AN: 150912 Hom.: 7740 Cov.: 0 AF XY: 0.309 AC XY: 22758 AN XY: 73762

African (AFR) AF: 0.254 AC: 10524 AN: 41356

American (AMR) AF: 0.364 AC: 5507 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1187 AN: 3438

East Asian (EAS) AF: 0.236 AC: 1216 AN: 5154

South Asian (SAS) AF: 0.279 AC: 1340 AN: 4810

European-Finnish (FIN) AF: 0.231 AC: 2421 AN: 10492

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 23972 AN: 67240

Other (OTH) AF: 0.299 AC: 627 AN: 2098

Alfa AF: 0.342 Hom.: 1050

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

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: rs140759;

hg19: chr6-120389455;