rs13030978

chr2-191252512-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001130158.3(MYO1B):c.-10+6886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,192 control chromosomes in the GnomAD database, including 4,959 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 0.24 (4959 hom., cov: 32)
• Consequence: MYO1B NM_001130158.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

MYO1B (HGNC:7596): (myosin IB) Enables ATP binding activity; actin filament binding activity; and microfilament motor activity. Involved in actin filament organization and post-Golgi vesicle-mediated transport. Located in several cellular components, including actin filament; endosome; and perinuclear region of cytoplasm. Colocalizes with trans-Golgi network membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO1B	NM_001130158.3	c.-10+6886C>T		intron_variant		ENST00000392318.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1B	ENST00000392318.8	c.-10+6886C>T		intron_variant		1	NM_001130158.3	P1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36880 AN: 152074 Hom.: 4947 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.242 AC: 36903 AN: 152192 Hom.: 4959 Cov.: 32 AF XY: 0.241 AC XY: 17937 AN XY: 74398

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.301

Alfa AF: 0.264 Hom.: 2208

Bravo AF: 0.244

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.1
Dann	Benign	0.36

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: rs13030978; hg19: chr2-192117238;