19-40868653-CAA-CAAA

Variant names:

• chr19-40868653-C-CA
• rs34226463
• ENST00000601627.1:n.118-23338_118-23337insA

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.118-23338_118-23337insA 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 0.67 (31706 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 (EAS) allele frequency at 95% confidence interval = 0.691 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_118-23337insA		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.668 AC: 94238 AN: 141022 Hom.: 31697 Cov.: 0

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.578

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.668 AC: 94266 AN: 141078 Hom.: 31706 Cov.: 0 AF XY: 0.671 AC XY: 45717 AN XY: 68102

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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;