chrX-53122914-G-T

Variant names:

• chrX-53122914-G-T
• rs10127016
• NM_001397448.1:c.-804-555G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001397448.1(KANTR):​c.-804-555G>T variant causes a intron 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 0.76 (22724 hom., 24296 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: KANTR NM_001397448.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• Publications: 3 publications found

Genes affected

KANTR (HGNC:49510): (KANTR integral membrane protein) This gene is thought to produce a functional long non-coding RNA. Mutation of this locus in mouse causes tremors and spastic movements, suggesting a role for this gene in neurological development or function. [provided by RefSeq, Feb 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KANTR	NM_001397448.1	c.-804-555G>T		intron_variant	Intron 2 of 2	ENST00000604062.7	NP_001384377.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KANTR	ENST00000604062.7	c.-804-555G>T		intron_variant	Intron 2 of 2	5	NM_001397448.1	ENSP00000492284.1

Frequencies

GnomAD3 genomes AF: 0.755 AC: 83037 AN: 109913 Hom.: 22727 Cov.: 22

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.795

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.779

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.755 AC: 83062 AN: 109962 Hom.: 22724 Cov.: 22 AF XY: 0.754 AC XY: 24296 AN XY: 32226

African (AFR) AF: 0.584 AC: 17695 AN: 30294

American (AMR) AF: 0.859 AC: 8761 AN: 10203

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2176 AN: 2622

East Asian (EAS) AF: 0.919 AC: 3223 AN: 3506

South Asian (SAS) AF: 0.782 AC: 2039 AN: 2606

European-Finnish (FIN) AF: 0.758 AC: 4282 AN: 5646

Middle Eastern (MID) AF: 0.820 AC: 178 AN: 217

European-Non Finnish (NFE) AF: 0.819 AC: 43158 AN: 52709

Other (OTH) AF: 0.776 AC: 1154 AN: 1488

Alfa AF: 0.794 Hom.: 111152

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.2
DANN	Benign	0.56
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10127016; hg19: chrX-53152096;