ENST00000582441.1:c.439-2379_439-2378insTAAA

Variant names:

• chr17-27801260-T-TTTTA
• rs12720460
• ENST00000582441.1:c.439-2379_439-2378insTAAA

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.439-2379_439-2378insTAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 151,986 control chromosomes in the GnomAD database, including 975 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (975 hom., cov: 30)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 2 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582441.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266202	ENST00000582441.1	TSL:4	c.439-2379_439-2378insTAAA		intron	N/A	ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16563 AN: 151866 Hom.: 976 Cov.: 30

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0528

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.109 AC: 16577 AN: 151986 Hom.: 975 Cov.: 30 AF XY: 0.107 AC XY: 7922 AN XY: 74286

African (AFR) AF: 0.130 AC: 5392 AN: 41404

American (AMR) AF: 0.0879 AC: 1342 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.0534 AC: 257 AN: 4810

European-Finnish (FIN) AF: 0.0753 AC: 797 AN: 10578

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7719 AN: 67958

Other (OTH) AF: 0.128 AC: 270 AN: 2110

Alfa AF: 0.0241 Hom.: 15

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12720460; hg19: chr17-26128286;