17-32550640-C-T

Variant names:

• chr17-32550640-C-T
• rs225190
• NM_015194.3:c.2864+54447G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015194.3(MYO1D):​c.2864+54447G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 151,964 control chromosomes in the GnomAD database, including 34,537 homozygotes. 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: 𝑓 0.67 (34537 hom., cov: 31)
• Consequence: MYO1D NM_015194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 20 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

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.2864+54447G>A		intron	N/A	NP_056009.1	O94832
	MYO1D	NM_001411088.1		c.2600+54447G>A		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.2864+54447G>A		intron	N/A	ENSP00000324527.5	O94832
	MYO1D	ENST00000889850.1		c.2921+54447G>A		intron	N/A	ENSP00000559909.1
	MYO1D	ENST00000889848.1		c.2912+54447G>A		intron	N/A	ENSP00000559907.1

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100989 AN: 151846 Hom.: 34480 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.665 AC: 101114 AN: 151964 Hom.: 34537 Cov.: 31 AF XY: 0.659 AC XY: 48955 AN XY: 74244

African (AFR) AF: 0.824 AC: 34186 AN: 41486

American (AMR) AF: 0.619 AC: 9435 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2194 AN: 3472

East Asian (EAS) AF: 0.675 AC: 3485 AN: 5160

South Asian (SAS) AF: 0.723 AC: 3481 AN: 4816

European-Finnish (FIN) AF: 0.473 AC: 4969 AN: 10510

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41171 AN: 67958

Other (OTH) AF: 0.654 AC: 1375 AN: 2104

Alfa AF: 0.621 Hom.: 101917

Bravo AF: 0.679

Asia WGS AF: 0.714 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	4.7
DANN	Benign	0.86
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs225190; hg19: chr17-30877658;