rs10497718

Positions:

• chr2-191414819-G-A

Variant summary

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

The NM_001130158.3(MYO1B):​c.3159+150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 703,468 control chromosomes in the GnomAD database, including 736 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 0.054 (384 hom., cov: 33)
  • Exomes 𝑓: 0.026 (352 hom.)
• Consequence: MYO1B NM_001130158.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO1B	NM_001130158.3	c.3159+150G>A		intron_variant		ENST00000392318.8	NP_001123630.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO1B	ENST00000392318.8	c.3159+150G>A		intron_variant		1	NM_001130158.3	ENSP00000376132	P1

Frequencies

GnomAD3 genomes AF: 0.0543 AC: 8262 AN: 152088 Hom.: 381 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.0178

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0642

GnomAD4 exome AF: 0.0259 AC: 14258 AN: 551262 Hom.: 352 AF XY: 0.0265 AC XY: 7351 AN XY: 277588

Gnomad4 AFR exome AF: 0.120

Gnomad4 AMR exome AF: 0.0397

Gnomad4 ASJ exome AF: 0.0985

Gnomad4 EAS exome AF: 0.000696

Gnomad4 SAS exome AF: 0.0383

Gnomad4 FIN exome AF: 0.0179

Gnomad4 NFE exome AF: 0.0203

Gnomad4 OTH exome AF: 0.0396

GnomAD4 genome AF: 0.0544 AC: 8274 AN: 152206 Hom.: 384 Cov.: 33 AF XY: 0.0545 AC XY: 4052 AN XY: 74396

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0449

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0422

Gnomad4 FIN AF: 0.0178

Gnomad4 NFE AF: 0.0224

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0382 Hom.: 56

Bravo AF: 0.0597

Asia WGS AF: 0.0340 AC: 119 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.15
DANN	Benign	0.46

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: rs10497718; hg19: chr2-192279545;