19-40819292-T-A

Variant names:

• chr19-40819292-T-A
• rs537785857
• ENST00000601627.1:n.117+17877T>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000601627.1(ENSG00000268797):​n.117+17877T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000073 (0 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 0 publications found

Genes affected

ENSG00000268797 (HGNC:):

CYP2F2P (HGNC:18851): (cytochrome P450 family 2 subfamily F member 2, pseudogene)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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.117+17877T>A		intron	N/A	ENSP00000469533.1	M0QY20
	CYP2F2P	ENST00000437853.1	TSL:6	n.874-389A>T		intron	N/A
	ENSG00000293114	ENST00000641827.1		n.519-393A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000732 AC: 1 AN: 136556 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000233

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000732 AC: 1 AN: 136664 Hom.: 0 Cov.: 31 AF XY: 0.0000150 AC XY: 1 AN XY: 66558

African (AFR) AF: 0.00 AC: 0 AN: 40614

American (AMR) AF: 0.00 AC: 0 AN: 12352

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3192

East Asian (EAS) AF: 0.000233 AC: 1 AN: 4286

South Asian (SAS) AF: 0.00 AC: 0 AN: 3932

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9442

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 59936

Other (OTH) AF: 0.00 AC: 0 AN: 1878

Alfa AF: 0.000109 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.21
PhyloP100		1.2

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: rs537785857;

hg19: chr19-41325197;