NM_001397448.1:c.-804-555G>C

Variant names:

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

Variant summary

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

The NM_001397448.1(KANTR):​c.-804-555G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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)
• 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001397448.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KANTR	NM_001397448.1	MANE Select	c.-804-555G>C		intron	N/A	NP_001384377.1	A0A1W2PQU2
	KANTR	NM_001397450.1		c.-804-555G>C		intron	N/A	NP_001384379.1	A0A1W2PQU2
	KANTR	NM_001397451.1		c.-804-555G>C		intron	N/A	NP_001384380.1	A0A1W2PQU2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KANTR	ENST00000604062.7	TSL:5 MANE Select	c.-804-555G>C		intron	N/A	ENSP00000492284.1	A0A1W2PQU2
	KANTR	ENST00000860106.1		c.-804-555G>C		intron	N/A	ENSP00000530165.1
	KANTR	ENST00000860107.1		c.-804-555G>C		intron	N/A	ENSP00000530166.1

Frequencies

GnomAD3 genomes Cov.: 22

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

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.22
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;