rs10492418

Variant names:

• chr13-108728378-A-C
• rs10492418
• NM_001198950.3:c.507+795A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-108728378-A-C
• chr13-108728378-A-T

Variant summary

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

The NM_001198950.3(MYO16):​c.507+795A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,966 control chromosomes in the GnomAD database, including 15,390 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 0.44 (15390 hom., cov: 31)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 5 publications found

Genes affected

MYO16 (HGNC:29822): (myosin XVI) This gene encodes an unconventional myosin protein. The encoded protein has been proposed to act as a serine/threonine phosphatase-1 targeting or regulatory subunit. Studies in a rat cell line suggest that this protein may regulate cell cycle progression. A variant within this gene may be associated with susceptibility to schizophrenia and elevated expression of this gene has been observed in the frontal cortex of human schizophrenia patients. [provided by RefSeq, Mar 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001198950.3. 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
	MYO16	NM_001198950.3	MANE Select	c.507+795A>C		intron	N/A	NP_001185879.1	F8W883
	MYO16	NM_015011.3		c.441+795A>C		intron	N/A	NP_055826.1	Q9Y6X6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	ENST00000457511.7	TSL:1 MANE Select	c.507+795A>C		intron	N/A	ENSP00000401633.3	F8W883
	MYO16	ENST00000356711.7	TSL:1	c.441+795A>C		intron	N/A	ENSP00000349145.2	Q9Y6X6-1
	MYO16	ENST00000251041.10	TSL:5	c.441+795A>C		intron	N/A	ENSP00000251041.5	Q9Y6X6-3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66209 AN: 151846 Hom.: 15381 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.436 AC: 66242 AN: 151966 Hom.: 15390 Cov.: 31 AF XY: 0.429 AC XY: 31849 AN XY: 74274

African (AFR) AF: 0.299 AC: 12374 AN: 41440

American (AMR) AF: 0.408 AC: 6233 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3468

East Asian (EAS) AF: 0.189 AC: 974 AN: 5162

South Asian (SAS) AF: 0.406 AC: 1957 AN: 4820

European-Finnish (FIN) AF: 0.444 AC: 4677 AN: 10530

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36739 AN: 67964

Other (OTH) AF: 0.459 AC: 967 AN: 2106

Alfa AF: 0.467 Hom.: 19972

Bravo AF: 0.422

Asia WGS AF: 0.332 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.70
PhyloP100		-0.16
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: rs10492418; hg19: chr13-109380726;