chr17-27801260-T-TTTTA

Position:

• chr17-27801260-T-TTTTA

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/exons	MANE	Protein	UniProt
		n.27801260_27801261insTTTA		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.439-2379_439-2378insTAAA		intron_variant		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;