2-170380611-C-G

Position:

• chr2-170380611-C-G

Variant summary

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

The NM_138995.5(MYO3B):​c.972-1405C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,146 control chromosomes in the GnomAD database, including 1,337 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 0.10 (1337 hom., cov: 33)
• Consequence: MYO3B NM_138995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

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]

MYO3B-AS1 (HGNC:40713): (MYO3B antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO3B	NM_138995.5	c.972-1405C>G		intron_variant		ENST00000408978.9	NP_620482.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO3B	ENST00000408978.9	c.972-1405C>G		intron_variant		1	NM_138995.5	ENSP00000386213	P1
MYO3B-AS1	ENST00000625968.2	n.196+3216G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15478 AN: 152030 Hom.: 1334 Cov.: 33

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.102 AC: 15491 AN: 152146 Hom.: 1337 Cov.: 33 AF XY: 0.106 AC XY: 7866 AN XY: 74376

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0884

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0402 Hom.: 24

Bravo AF: 0.105

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.70

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: rs10497367; hg19: chr2-171237121;