17-27801260-TTTTA-TTTTATTTA

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.439-2379_439-2378insTAAA		intron_variant	Intron 4 of 4	4		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

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0534

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.128

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12720460; hg19: chr17-26128286;