6-34246544-CC-TT

Variant names:

• chr6-34246544-CC-TT
• ENST00000636500.1:c.449_450delGGinsAA
• SMIM29 p.Gly150Glu

Variant summary

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

The ENST00000636500.1(SMIM29):​c.449_450delGGinsAA​(p.Gly150Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMIM29 ENST00000636500.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 0 publications found

Genes affected

SMIM29 (HGNC:1340): (small integral membrane protein 29) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636500.1. 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
	SMIM29	NM_001008703.4	MANE Select	c.*258_*259delGGinsAA		3_prime_UTR	Exon 5 of 5	NP_001008703.2	Q86T20-1
	SMIM29	NM_178508.6		c.*258_*259delGGinsAA		3_prime_UTR	Exon 5 of 5	NP_848603.3	Q86T20-1
	SMIM29	NM_001008704.4		c.*258_*259delGGinsAA		3_prime_UTR	Exon 5 of 5	NP_001008704.2	Q86T20-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM29	ENST00000636500.1	TSL:1	c.449_450delGGinsAA	p.Gly150Glu	missense	N/A	ENSP00000489784.1	A0A2U3TZT1
	SMIM29	ENST00000476320.6	TSL:2 MANE Select	c.*258_*259delGGinsAA		3_prime_UTR	Exon 5 of 5	ENSP00000417604.2	Q86T20-1
	SMIM29	ENST00000481533.5	TSL:1	c.*258_*259delGGinsAA		3_prime_UTR	Exon 5 of 5	ENSP00000418062.2	Q86T20-1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.28

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: chr6-34214321;