rs2098802

Variant names:

• chr2-170195673-G-C
• rs2098802
• NM_138995.5:c.3-3535G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-170195673-G-C
• chr2-170195673-G-T

Variant summary

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

The NM_138995.5(MYO3B):​c.3-3535G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,000 control chromosomes in the GnomAD database, including 10,179 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 0.36 (10179 hom., cov: 31)
• Consequence: MYO3B NM_138995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 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]

ENSG00000308085 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138995.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO3B	NM_138995.5	MANE Select	c.3-3535G>C		intron	N/A	NP_620482.3
	MYO3B	NM_001083615.4		c.3-3535G>C		intron	N/A	NP_001077084.2
	MYO3B	NR_045682.2		n.144-3535G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO3B	ENST00000408978.9	TSL:1 MANE Select	c.3-3535G>C		intron	N/A	ENSP00000386213.4
	MYO3B	ENST00000409044.7	TSL:1	c.3-3535G>C		intron	N/A	ENSP00000386497.3
	MYO3B	ENST00000409940.6	TSL:1	n.146-3535G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55219 AN: 151880 Hom.: 10182 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.363 AC: 55241 AN: 152000 Hom.: 10179 Cov.: 31 AF XY: 0.359 AC XY: 26687 AN XY: 74292

African (AFR) AF: 0.394 AC: 16347 AN: 41460

American (AMR) AF: 0.285 AC: 4344 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3470

East Asian (EAS) AF: 0.159 AC: 819 AN: 5166

South Asian (SAS) AF: 0.368 AC: 1770 AN: 4816

European-Finnish (FIN) AF: 0.342 AC: 3621 AN: 10578

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25883 AN: 67934

Other (OTH) AF: 0.351 AC: 739 AN: 2106

Alfa AF: 0.213 Hom.: 436

Bravo AF: 0.357

Asia WGS AF: 0.261 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.44
PhyloP100		0.36
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: rs2098802; hg19: chr2-171052183;