4-107956127-C-A

Variant names:

• chr4-107956127-C-A
• rs4607298
• ENST00000513071.2:n.263+22593G>T

Variant summary

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

The ENST00000513071.2(CYP2U1-AS1):​n.263+22593G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,968 control chromosomes in the GnomAD database, including 29,747 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 0.62 (29747 hom., cov: 32)
• Consequence: CYP2U1-AS1 ENST00000513071.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 3 publications found

Genes affected

CYP2U1-AS1 (HGNC:54817): (CYP2U1 and SGMS2 antisense RNA 1)

LOC107986298 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986298	XR_001741784.2	n.204+22593G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2U1-AS1	ENST00000513071.2	n.263+22593G>T		intron_variant	Intron 1 of 1	3
CYP2U1-AS1	ENST00000656249.1	n.80+22593G>T		intron_variant	Intron 1 of 9
CYP2U1-AS1	ENST00000658105.4	n.194+33441G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94323 AN: 151850 Hom.: 29713 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.621 AC: 94408 AN: 151968 Hom.: 29747 Cov.: 32 AF XY: 0.612 AC XY: 45467 AN XY: 74282

African (AFR) AF: 0.607 AC: 25172 AN: 41482

American (AMR) AF: 0.557 AC: 8510 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2633 AN: 3466

East Asian (EAS) AF: 0.312 AC: 1609 AN: 5150

South Asian (SAS) AF: 0.522 AC: 2511 AN: 4814

European-Finnish (FIN) AF: 0.603 AC: 6340 AN: 10522

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45416 AN: 67942

Other (OTH) AF: 0.655 AC: 1381 AN: 2110

Alfa AF: 0.642 Hom.: 3928

Bravo AF: 0.617

Asia WGS AF: 0.483 AC: 1678 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.2
DANN	Benign	0.68
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4607298; hg19: chr4-108877283; COSMIC: COSV107411692;