rs76478271

Variant names:

• chr19-40819294-T-A
• rs76478271
• ENST00000601627.1:n.117+17879T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000601627.1(ENSG00000268797):​n.117+17879T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,000 control chromosomes in the GnomAD database, including 3,955 homozygotes. 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 0.15 (3955 hom., cov: 30)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 3 publications found

Genes affected

ENSG00000268797 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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.117+17879T>A		intron	N/A	ENSP00000469533.1	M0QY20
	CYP2F2P	ENST00000437853.1	TSL:6	n.874-391A>T		intron	N/A
	ENSG00000293114	ENST00000641827.1		n.519-395A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23032 AN: 150880 Hom.: 3936 Cov.: 30

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0343

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.153 AC: 23088 AN: 151000 Hom.: 3955 Cov.: 30 AF XY: 0.146 AC XY: 10779 AN XY: 73690

African (AFR) AF: 0.427 AC: 17571 AN: 41138

American (AMR) AF: 0.0908 AC: 1380 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.0950 AC: 328 AN: 3454

East Asian (EAS) AF: 0.00118 AC: 6 AN: 5106

South Asian (SAS) AF: 0.0344 AC: 164 AN: 4774

European-Finnish (FIN) AF: 0.0144 AC: 149 AN: 10336

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0452 AC: 3059 AN: 67708

Other (OTH) AF: 0.151 AC: 316 AN: 2086

Alfa AF: 0.116 Hom.: 290

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.23
PhyloP100		0.28

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

Other links and lift over

dbSNP: rs76478271; hg19: chr19-41325199;