chr19-40868653-CA-C

Variant names:

• chr19-40868653-CA-C
• rs34226463
• ENST00000601627.1:n.118-23337delA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000601627.1(ENSG00000268797):​n.118-23337delA 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 0.00022 (0 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: Uncertain_significance. The variant received 0 ACMG points.

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.118-23337delA		intron	N/A	ENSP00000469533.1	M0QY20

Frequencies

GnomAD3 genomes AF: 0.000220 AC: 31 AN: 141122 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000710

Gnomad ASJ AF: 0.000300

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00107

Gnomad MID AF: 0.00340

Gnomad NFE AF: 0.000217

Gnomad OTH AF: 0.000521

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

GnomAD4 genome AF: 0.000220 AC: 31 AN: 141176 Hom.: 0 Cov.: 0 AF XY: 0.000220 AC XY: 15 AN XY: 68150

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000103 AC: 4 AN: 38732

American (AMR) AF: 0.0000709 AC: 1 AN: 14100

Ashkenazi Jewish (ASJ) AF: 0.000300 AC: 1 AN: 3330

East Asian (EAS) AF: 0.00 AC: 0 AN: 4518

South Asian (SAS) AF: 0.000231 AC: 1 AN: 4338

European-Finnish (FIN) AF: 0.00107 AC: 9 AN: 8408

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 274

European-Non Finnish (NFE) AF: 0.000217 AC: 14 AN: 64650

Other (OTH) AF: 0.000519 AC: 1 AN: 1928

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000000921905), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 1219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-3.5

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

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;