rs35335725

Variant names:

• chr17-41059237-A-ATG
• rs35335725
• ENST00000815517.1:n.220-1062_220-1061insTG

Variant summary

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

The ENST00000815517.1(ENSG00000306126):​n.220-1062_220-1061insTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 176,298 control chromosomes in the GnomAD database, including 3,787 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (3723 hom., cov: 30)
  • Exomes 𝑓: 0.015 (64 hom.)
• Consequence: ENSG00000306126 ENST00000815517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 1 publications found

Genes affected

ENSG00000306126 (HGNC:):

KRTAP2-3 (HGNC:18906): (keratin associated protein 2-3) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815517.1. 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
	KRTAP2-3	NM_001165252.2	MANE Select	c.*426_*427insCA		downstream_gene	N/A	NP_001158724.1	P0C7H8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306126	ENST00000815517.1		n.220-1062_220-1061insTG		intron	N/A
	ENSG00000306126	ENST00000815518.1		n.160-1062_160-1061insTG		intron	N/A
	ENSG00000306126	ENST00000815519.1		n.333-1062_333-1061insTG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18078 AN: 151382 Hom.: 3709 Cov.: 30

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.00417

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00174

Gnomad OTH AF: 0.0809

GnomAD4 exome AF: 0.0146 AC: 362 AN: 24798 Hom.: 64 Cov.: 0 AF XY: 0.0129 AC XY: 159 AN XY: 12332

African (AFR) AF: 0.373 AC: 277 AN: 742

American (AMR) AF: 0.0123 AC: 20 AN: 1630

Ashkenazi Jewish (ASJ) AF: 0.00126 AC: 1 AN: 796

East Asian (EAS) AF: 0.00189 AC: 2 AN: 1056

South Asian (SAS) AF: 0.00181 AC: 1 AN: 552

European-Finnish (FIN) AF: 0.00115 AC: 1 AN: 872

Middle Eastern (MID) AF: 0.0156 AC: 2 AN: 128

European-Non Finnish (NFE) AF: 0.000857 AC: 15 AN: 17502

Other (OTH) AF: 0.0283 AC: 43 AN: 1520

GnomAD4 genome AF: 0.120 AC: 18139 AN: 151500 Hom.: 3723 Cov.: 30 AF XY: 0.116 AC XY: 8564 AN XY: 74096

African (AFR) AF: 0.417 AC: 17171 AN: 41208

American (AMR) AF: 0.0419 AC: 636 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 8 AN: 3464

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5186

South Asian (SAS) AF: 0.00376 AC: 18 AN: 4792

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10572

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00174 AC: 118 AN: 67806

Other (OTH) AF: 0.0801 AC: 168 AN: 2098

Alfa AF: 0.109 Hom.: 259

Bravo AF: 0.138

Asia WGS AF: 0.0270 AC: 92 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs35335725; hg19: chr17-39215489;