2-170242115-G-A

Variant names:

• chr2-170242115-G-A
• rs10497360
• NM_138995.5:c.749+5979G>A

Variant summary

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

The NM_138995.5(MYO3B):​c.749+5979G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,232 control chromosomes in the GnomAD database, including 507 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 0.063 (507 hom., cov: 32)
• Consequence: MYO3B NM_138995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 0 publications found

Genes affected

MYO3B (HGNC:15576): (myosin IIIB) This gene encodes one of the class III myosins. Myosins are ATPases, activated by actin, that move along actin filaments in the cell. This class of myosins are characterized by an amino-terminal kinase domain and shown to be present in photoreceptors. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO3B	NM_138995.5	c.749+5979G>A		intron_variant	Intron 7 of 34	ENST00000408978.9	NP_620482.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO3B	ENST00000408978.9	c.749+5979G>A		intron_variant	Intron 7 of 34	1	NM_138995.5	ENSP00000386213.4

Frequencies

GnomAD3 genomes AF: 0.0633 AC: 9633 AN: 152114 Hom.: 508 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.0275

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0316

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0633 AC: 9635 AN: 152232 Hom.: 507 Cov.: 32 AF XY: 0.0618 AC XY: 4603 AN XY: 74432

African (AFR) AF: 0.148 AC: 6131 AN: 41514

American (AMR) AF: 0.0392 AC: 599 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4818

European-Finnish (FIN) AF: 0.0275 AC: 292 AN: 10610

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

European-Non Finnish (NFE) AF: 0.0316 AC: 2148 AN: 68032

Other (OTH) AF: 0.0583 AC: 123 AN: 2110

Alfa AF: 0.0524 Hom.: 47

Bravo AF: 0.0665

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	9.5
DANN	Benign	0.56
PhyloP100		0.13
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: rs10497360; hg19: chr2-171098625;