chr19-40868653-C-CAA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601627.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268797	ENST00000601627.1	TSL:3	n.118-23338_118-23337insAA		intron	N/A	ENSP00000469533.1	M0QY20

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

African (AFR) AF: 0.247 AC: 9537 AN: 38680

American (AMR) AF: 0.139 AC: 1955 AN: 14060

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 304 AN: 3326

East Asian (EAS) AF: 0.0678 AC: 306 AN: 4516

South Asian (SAS) AF: 0.0574 AC: 249 AN: 4338

European-Finnish (FIN) AF: 0.0419 AC: 352 AN: 8392

Middle Eastern (MID) AF: 0.157 AC: 43 AN: 274

European-Non Finnish (NFE) AF: 0.0763 AC: 4930 AN: 64576

Other (OTH) AF: 0.140 AC: 268 AN: 1920

Alfa AF: 0.0541 Hom.: 1219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-3.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs34226463; hg19: chr19-41374558;