17-29144935-G-A

Variant names:

• chr17-29144935-G-A
• rs8067041
• NM_078471.4:c.999+21007C>T

Variant summary

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

The NM_078471.4(MYO18A):​c.999+21007C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,012 control chromosomes in the GnomAD database, including 16,688 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 0.44 (16688 hom., cov: 32)
• Consequence: MYO18A NM_078471.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 2 publications found

Genes affected

MYO18A (HGNC:31104): (myosin XVIIIA) The protein encoded by this gene can bind GOLPH3, linking the Golgi to the cytoskeleton and influencing Golgi membrane trafficking. The encoded protein is also part of a complex that assembles lamellar actomyosin bundles and may be required for cell migration. [provided by RefSeq, Oct 2016]

ENSG00000263709 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_078471.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO18A	NM_078471.4	MANE Select	c.999+21007C>T		intron	N/A	NP_510880.2
	MYO18A	NM_001346765.2		c.1000-20247C>T		intron	N/A	NP_001333694.1
	MYO18A	NM_001346766.2		c.1000-20247C>T		intron	N/A	NP_001333695.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO18A	ENST00000527372.7	TSL:1 MANE Select	c.999+21007C>T		intron	N/A	ENSP00000437073.1
	MYO18A	ENST00000533112.5	TSL:1	c.999+21007C>T		intron	N/A	ENSP00000435932.1
	MYO18A	ENST00000704659.1		c.1000-20247C>T		intron	N/A	ENSP00000515984.1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67276 AN: 151894 Hom.: 16663 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.443 AC: 67350 AN: 152012 Hom.: 16688 Cov.: 32 AF XY: 0.440 AC XY: 32658 AN XY: 74296

African (AFR) AF: 0.676 AC: 27995 AN: 41432

American (AMR) AF: 0.353 AC: 5396 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3468

East Asian (EAS) AF: 0.588 AC: 3043 AN: 5174

South Asian (SAS) AF: 0.513 AC: 2475 AN: 4826

European-Finnish (FIN) AF: 0.280 AC: 2956 AN: 10544

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22759 AN: 67962

Other (OTH) AF: 0.435 AC: 921 AN: 2116

Alfa AF: 0.419 Hom.: 2726

Bravo AF: 0.456

Asia WGS AF: 0.537 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.43
PhyloP100		-0.30
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: rs8067041; hg19: chr17-27471953;