NM_015194.3:c.2491-5_2491-4dupTT

Variant names:

• chr17-32653950-G-GAA
• NM_015194.3:c.2491-5_2491-4dupTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_015194.3(MYO1D):​c.2491-5_2491-4dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYO1D NM_015194.3 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.413
• Publications: 0 publications found

Genes affected

MYO1D (HGNC:7598): (myosin ID) Enables protein domain specific binding activity. Predicted to be involved in actin filament organization; early endosome to recycling endosome transport; and vesicle transport along actin filament. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

MYO1D-AS1 (HGNC:58309):

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 17-32653950-G-GAA is Benign according to our data. Variant chr17-32653950-G-GAA is described in ClinVar as Likely_benign. ClinVar VariationId is 2798127.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015194.3. 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
	MYO1D	NM_015194.3	MANE Select	c.2491-5_2491-4dupTT		splice_region intron	N/A	NP_056009.1	O94832
	MYO1D	NM_001303279.2		c.2491-5_2491-4dupTT		splice_region intron	N/A	NP_001290208.1	J3QRN6
	MYO1D	NM_001411088.1		c.2227-5_2227-4dupTT		splice_region intron	N/A	NP_001398017.1	K7EIG7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO1D	ENST00000318217.10	TSL:1 MANE Select	c.2491-4_2491-3insTT		splice_region intron	N/A	ENSP00000324527.5	O94832
	MYO1D	ENST00000889850.1		c.2548-4_2548-3insTT		splice_region intron	N/A	ENSP00000559909.1
	MYO1D	ENST00000889848.1		c.2539-4_2539-3insTT		splice_region intron	N/A	ENSP00000559907.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.41

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: chr17-30980968;