X-27863980-G-C

Variant names:

• chrX-27863980-G-C
• rs28940302
• ENST00000421897.1:n.88G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000421897.1(VKORC1P1):​n.88G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,054,587 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. 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 0.00016 (0 hom., 6 hem., cov: 23)
  • Exomes 𝑓: 0.000019 (0 hom. 9 hem.)
• Consequence: VKORC1P1 ENST00000421897.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.81
• Publications: 3 publications found

Genes affected

VKORC1P1 (HGNC:33182): (VKORC1 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BS2: High Hemizygotes in GnomAd4 at 6 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421897.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VKORC1P1	ENST00000421897.1	TSL:6	n.88G>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.000160 AC: 18 AN: 112404 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.000549

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000365

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000191 AC: 18 AN: 942138 Hom.: 0 Cov.: 26 AF XY: 0.0000310 AC XY: 9 AN XY: 289956

African (AFR) AF: 0.000709 AC: 15 AN: 21167

American (AMR) AF: 0.00 AC: 0 AN: 14141

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13360

East Asian (EAS) AF: 0.00 AC: 0 AN: 24044

South Asian (SAS) AF: 0.00 AC: 0 AN: 32702

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21833

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3202

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 771806

Other (OTH) AF: 0.0000752 AC: 3 AN: 39883

GnomAD4 genome AF: 0.000160 AC: 18 AN: 112449 Hom.: 0 Cov.: 23 AF XY: 0.000173 AC XY: 6 AN XY: 34613

African (AFR) AF: 0.000548 AC: 17 AN: 31031

American (AMR) AF: 0.00 AC: 0 AN: 10743

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2649

East Asian (EAS) AF: 0.00 AC: 0 AN: 3503

South Asian (SAS) AF: 0.000367 AC: 1 AN: 2726

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6156

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 215

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53213

Other (OTH) AF: 0.00 AC: 0 AN: 1529

Alfa AF: 0.0000615 Hom.: 0

Bravo AF: 0.000185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs28940302; hg19: chrX-27882097;