chr2-191379667-A-G

Variant names:

• chr2-191379667-A-G
• rs1517835
• NM_001130158.3:c.1186-1795A>G

Variant summary

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

The NM_001130158.3(MYO1B):​c.1186-1795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,092 control chromosomes in the GnomAD database, including 52,583 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 0.79 (52583 hom., cov: 32)
• Consequence: MYO1B NM_001130158.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 8 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130158.3. 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
	MYO1B	NM_001130158.3	MANE Select	c.1186-1795A>G		intron	N/A	NP_001123630.1
	MYO1B	NM_001161819.3		c.1186-1795A>G		intron	N/A	NP_001155291.1
	MYO1B	NM_001330237.2		c.1186-1795A>G		intron	N/A	NP_001317166.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO1B	ENST00000392318.8	TSL:1 MANE Select	c.1186-1795A>G		intron	N/A	ENSP00000376132.3
	MYO1B	ENST00000304164.8	TSL:1	c.1186-1795A>G		intron	N/A	ENSP00000306382.4
	MYO1B	ENST00000339514.8	TSL:1	c.1186-1795A>G		intron	N/A	ENSP00000341903.4

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119414 AN: 151974 Hom.: 52574 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.785 AC: 119441 AN: 152092 Hom.: 52583 Cov.: 32 AF XY: 0.789 AC XY: 58650 AN XY: 74358

African (AFR) AF: 0.353 AC: 14596 AN: 41402

American (AMR) AF: 0.820 AC: 12533 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3113 AN: 3472

East Asian (EAS) AF: 0.946 AC: 4901 AN: 5180

South Asian (SAS) AF: 0.953 AC: 4590 AN: 4814

European-Finnish (FIN) AF: 0.982 AC: 10416 AN: 10608

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66411 AN: 68020

Other (OTH) AF: 0.812 AC: 1717 AN: 2114

Alfa AF: 0.893 Hom.: 118232

Bravo AF: 0.753

Asia WGS AF: 0.911 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.84
PhyloP100		0.48
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: rs1517835; hg19: chr2-192244393;