rs8067041

chr17-29144935-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO18A	NM_078471.4	c.999+21007C>T		intron_variant		ENST00000527372.7
LOC124903967	XR_007065693.1	n.53+4409G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO18A	ENST00000527372.7	c.999+21007C>T		intron_variant		1	NM_078471.4	A1
	ENST00000582196.1	n.44+4409G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.435

Alfa AF: 0.413 Hom.: 2558

Bravo AF: 0.456

Asia WGS AF: 0.537 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.62
Dann	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs8067041; hg19: chr17-27471953;