rs10497718

Variant names:

• chr2-191414819-G-A
• rs10497718
• NM_001130158.3:c.3159+150G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYO1B	NM_001130158.3	c.3159+150G>A		intron_variant	Intron 29 of 30	ENST00000392318.8	NP_001123630.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO1B	ENST00000392318.8	c.3159+150G>A		intron_variant	Intron 29 of 30	1	NM_001130158.3	ENSP00000376132.3

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

African (AFR) AF: 0.120 AC: 1565 AN: 13042

American (AMR) AF: 0.0397 AC: 394 AN: 9916

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 1271 AN: 12902

East Asian (EAS) AF: 0.000696 AC: 18 AN: 25856

South Asian (SAS) AF: 0.0383 AC: 947 AN: 24720

European-Finnish (FIN) AF: 0.0179 AC: 540 AN: 30188

Middle Eastern (MID) AF: 0.0791 AC: 202 AN: 2554

European-Non Finnish (NFE) AF: 0.0203 AC: 8202 AN: 403800

Other (OTH) AF: 0.0396 AC: 1119 AN: 28284

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

African (AFR) AF: 0.124 AC: 5161 AN: 41522

American (AMR) AF: 0.0449 AC: 686 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5190

South Asian (SAS) AF: 0.0422 AC: 203 AN: 4812

European-Finnish (FIN) AF: 0.0178 AC: 189 AN: 10598

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0224 AC: 1523 AN: 68010

Other (OTH) AF: 0.0636 AC: 134 AN: 2108

Alfa AF: 0.0404 Hom.: 78

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
PhyloP100		-1.1
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: rs10497718; hg19: chr2-192279545;