rs4607298

Positions:

• chr4-107956127-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656249.1(CYP2U1-AS1):​n.80+22593G>T variant causes a intron, non coding transcript 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 ENST00000656249.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

Genes affected

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

LOC107986298 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107986298	XR_001741784.2	n.204+22593G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2U1-AS1	ENST00000656249.1	n.80+22593G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.655

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4607298; hg19: chr4-108877283;