2-127133887-T-TGGG

Variant names:

• chr2-127133887-T-TGGG
• rs59335482
• ENST00000726607.1:n.342-1373_342-1372insGGG

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-1373_342-1372insGGG 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 0.30 (7024 hom., cov: 0)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 21 publications found

Genes affected

ENSG00000294899 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726607.1. 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
	ENSG00000294899	ENST00000726607.1		n.342-1373_342-1372insGGG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45400 AN: 150912 Hom.: 6994 Cov.: 0

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.301 AC: 45478 AN: 151028 Hom.: 7024 Cov.: 0 AF XY: 0.298 AC XY: 21973 AN XY: 73774

African (AFR) AF: 0.349 AC: 14329 AN: 41066

American (AMR) AF: 0.336 AC: 5103 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1041 AN: 3458

East Asian (EAS) AF: 0.334 AC: 1709 AN: 5124

South Asian (SAS) AF: 0.212 AC: 1014 AN: 4788

European-Finnish (FIN) AF: 0.235 AC: 2446 AN: 10410

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.279 AC: 18889 AN: 67712

Other (OTH) AF: 0.294 AC: 614 AN: 2088

Alfa AF: 0.121 Hom.: 194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.40

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: rs59335482;

hg19: chr2-127891463;