Genetic Variant WDR91:p.Pro257Leu (chr7-135204388-AG-GA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_014149.4(WDR91):c.770_771delCTinsTC(p.Pro257Leu) 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.

Frequency

Genomes: not found (cov: 32)

Consequence

WDR91
NM_014149.4 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.50

Publications

0 publications found

Variant links:

Genes affected

WDR91 (HGNC:24997): (WD repeat domain 91) Enables phosphatidylinositol 3-kinase regulator activity. Involved in early endosome to late endosome transport; regulation of cellular protein catabolic process; and regulation of phosphatidylinositol 3-kinase activity. Located in cytosol; early endosome membrane; and late endosome membrane. Is extrinsic component of endosome membrane. [provided by Alliance of Genome Resources, Apr 2022]

WDR91 links:

ENSG00000231794 (HGNC:):

ENSG00000231794 links:

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new If you want to explore the variant's impact on the transcript NM_014149.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014149.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
WDR91	NM_014149.4	MANE Select	c.770_771delCTinsTC	p.Pro257Leu	missense	N/A	NP_054868.3
WDR91	NM_001362737.2		c.770_771delCTinsTC	p.Pro257Leu	missense	N/A	NP_001349666.1
WDR91	NM_001362736.2		c.770_771delCTinsTC	p.Pro257Leu	missense	N/A	NP_001349665.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
WDR91	ENST00000354475.5	TSL:1 MANE Select	c.770_771delCTinsTC	p.Pro257Leu	missense	N/A	ENSP00000346466.4	A4D1P6-1
WDR91	ENST00000423565.5	TSL:5	c.665_666delCTinsTC	p.Pro222Leu	missense	N/A	ENSP00000392555.1	C9J1X0
WDR91	ENST00000956716.1		c.770_771delCTinsTC	p.Pro257Leu	missense	N/A	ENSP00000626775.1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

6.5

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over