chrX-79323946-C-A

Position:

• chrX-79323946-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000422742.2(KIF4CP):​n.418-81C>A variant causes a intron, non coding transcript 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 0.82 (26161 hom., 26471 hem., cov: 22)
  • Exomes 𝑓: 0.86 (76950 hom. 85623 hem.)
  • Failed GnomAD Quality Control
• Consequence: KIF4CP ENST00000422742.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

KIF4CP (HGNC:13340): (kinesin family member 4C, pseudogene)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF4CP	ENST00000422742.2	n.418-81C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.820 AC: 89829 AN: 109602 Hom.: 26162 Cov.: 22 AF XY: 0.830 AC XY: 26427 AN XY: 31844

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.903

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.853

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.861 AC: 263743 AN: 306364 Hom.: 76950 Cov.: 3 AF XY: 0.862 AC XY: 85623 AN XY: 99292

Gnomad4 AFR exome AF: 0.699

Gnomad4 AMR exome AF: 0.776

Gnomad4 ASJ exome AF: 0.911

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.841

Gnomad4 FIN exome AF: 0.861

Gnomad4 NFE exome AF: 0.860

Gnomad4 OTH exome AF: 0.859

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.820 AC: 89870 AN: 109658 Hom.: 26161 Cov.: 22 AF XY: 0.830 AC XY: 26471 AN XY: 31910

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.855

Alfa AF: 0.846 Hom.: 7257

Bravo AF: 0.809

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.53
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1736656; hg19: chrX-78579443;