rs59335482

Variant names:

• chr2-127133887-T-TG
• rs59335482
• ENST00000726607.1:n.342-1373_342-1372insG

Your query was ambiguous. Multiple possible variants found:

• chr2-127133887-T-TG
• chr2-127133887-T-TGG
• chr2-127133887-T-TGGG
• chr2-127133887-T-TGGGG
• chr2-127133887-T-TGGGGG
• chr2-127133887-T-TGGGGGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000726607.1(ENSG00000294899):​n.342-1373_342-1372insG 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 0.0053 (4 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.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00534 (807/151232) while in subpopulation AFR AF = 0.0172 (707/41120). AF 95% confidence interval is 0.0161. There are 4 homozygotes in GnomAd4. There are 373 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 4 gene

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294899	ENST00000726607.1		n.342-1373_342-1372insG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00531 AC: 803 AN: 151114 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00191

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.000192

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.000797

Gnomad OTH AF: 0.00484

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

GnomAD4 genome AF: 0.00534 AC: 807 AN: 151232 Hom.: 4 Cov.: 0 AF XY: 0.00505 AC XY: 373 AN XY: 73882

African (AFR) AF: 0.0172 AC: 707 AN: 41120

American (AMR) AF: 0.00191 AC: 29 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.000289 AC: 1 AN: 3460

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5132

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4798

European-Finnish (FIN) AF: 0.000192 AC: 2 AN: 10432

Middle Eastern (MID) AF: 0.00685 AC: 2 AN: 292

European-Non Finnish (NFE) AF: 0.000797 AC: 54 AN: 67786

Other (OTH) AF: 0.00478 AC: 10 AN: 2090

Alfa AF: 0.000593 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

Other links and lift over

dbSNP: rs59335482; hg19: chr2-127891463;