NM_001198950.3:c.507+2188A>C

Variant names:

• chr13-108729771-A-C
• rs932678
• NM_001198950.3:c.507+2188A>C

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+2188A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,284 control chromosomes in the GnomAD database, including 5,354 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 0.24 (5354 hom., cov: 33)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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+2188A>C		intron	N/A	NP_001185879.1	F8W883
	MYO16	NM_015011.3		c.441+2188A>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+2188A>C		intron	N/A	ENSP00000401633.3	F8W883
	MYO16	ENST00000356711.7	TSL:1	c.441+2188A>C		intron	N/A	ENSP00000349145.2	Q9Y6X6-1
	MYO16	ENST00000251041.10	TSL:5	c.441+2188A>C		intron	N/A	ENSP00000251041.5	Q9Y6X6-3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35780 AN: 151170 Hom.: 5341 Cov.: 33

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.237 AC: 35794 AN: 151284 Hom.: 5354 Cov.: 33 AF XY: 0.247 AC XY: 18301 AN XY: 73954

African (AFR) AF: 0.0762 AC: 3107 AN: 40776

American (AMR) AF: 0.354 AC: 5391 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2836 AN: 5144

South Asian (SAS) AF: 0.305 AC: 1468 AN: 4812

European-Finnish (FIN) AF: 0.365 AC: 3852 AN: 10556

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17486 AN: 67970

Other (OTH) AF: 0.235 AC: 496 AN: 2110

Alfa AF: 0.238 Hom.: 1871

Bravo AF: 0.229

Asia WGS AF: 0.383 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.4
DANN	Benign	0.78
PhyloP100		-0.20
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: rs932678; hg19: chr13-109382119;