X-79323946-C-G

Variant names:

• chrX-79323946-C-G
• rs1736656

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: KIF4CP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF4CP		n.79323946C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF4CP	ENST00000422742.2	n.418-81C>G		intron_variant	Intron 1 of 2	6

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 306795 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 99331

African (AFR) AF: 0.00 AC: 0 AN: 9100

American (AMR) AF: 0.00 AC: 0 AN: 13670

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8891

East Asian (EAS) AF: 0.00 AC: 0 AN: 20545

South Asian (SAS) AF: 0.00 AC: 0 AN: 24100

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26350

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1452

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 184913

Other (OTH) AF: 0.00 AC: 0 AN: 17774

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.25
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1736656; hg19: chrX-78579443;