19-40868653-CAA-CAAAA

Variant names:

• chr19-40868653-C-CAA
• rs34226463
• ENST00000601627.1:n.118-23338_118-23337insAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000601627.1(ENSG00000268797):​n.118-23338_118-23337insAA 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 0.13 (1735 hom., cov: 0)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 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
ENSG00000268797	ENST00000601627.1	n.118-23338_118-23337insAA		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 18003 AN: 140928 Hom.: 1733 Cov.: 0

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.0880

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.0764

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.128 AC: 18023 AN: 140980 Hom.: 1735 Cov.: 0 AF XY: 0.124 AC XY: 8445 AN XY: 68048

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0914

Gnomad4 EAS AF: 0.0678

Gnomad4 SAS AF: 0.0574

Gnomad4 FIN AF: 0.0419

Gnomad4 NFE AF: 0.0763

Gnomad4 OTH AF: 0.140

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: rs34226463; hg19: chr19-41374558;