chr6-152756195-AAC-TCG

Variant names:

• chr6-152756195-AAC-TCG
• NM_003381.4:c.397_399delAACinsTCG
• VIP p.Asn133Ser

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003381.4(VIP):​c.397_399delAACinsTCG​(p.Asn133Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Synonymous variant affecting the same amino acid position (i.e. N133N) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: VIP NM_003381.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.13
• Publications: 0 publications found

Genes affected

VIP (HGNC:12693): (vasoactive intestinal peptide) The protein encoded by this gene belongs to the glucagon family. It stimulates myocardial contractility, causes vasodilation, increases glycogenolysis, lowers arterial blood pressure and relaxes the smooth muscle of trachea, stomach and gall bladder. The protein also acts as an antimicrobial peptide with antibacterial and antifungal activity. Alternative splicing occurs at this locus and two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Nov 2014]

LINC02840 (HGNC:54374): (long intergenic non-protein coding RNA 2840)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003381.4. 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
	VIP	NM_003381.4	MANE Select	c.397_399delAACinsTCG	p.Asn133Ser	missense	N/A	NP_003372.1	P01282-1
	VIP	NM_194435.3		c.394_396delAACinsTCG	p.Asn132Ser	missense	N/A	NP_919416.1	P01282-2
	LINC02840	NR_183504.1		n.3073_3075delGTTinsCGA		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIP	ENST00000367244.8	TSL:1 MANE Select	c.397_399delAACinsTCG	p.Asn133Ser	missense	N/A	ENSP00000356213.3	P01282-1
	VIP	ENST00000367243.7	TSL:1	c.394_396delAACinsTCG	p.Asn132Ser	missense	N/A	ENSP00000356212.3	P01282-2
	VIP	ENST00000897584.1		c.397_399delAACinsTCG	p.Asn133Ser	missense	N/A	ENSP00000567643.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-153077330;