chr13-108779145-T-C

Variant names:

• chr13-108779145-T-C
• rs878536
• NM_001198950.3:c.508-6490T>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.508-6490T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 151,976 control chromosomes in the GnomAD database, including 632 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 0.080 (632 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.508-6490T>C		intron_variant	Intron 4 of 34	ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.508-6490T>C		intron_variant	Intron 4 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.442-6490T>C		intron_variant	Intron 4 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.442-6490T>C		intron_variant	Intron 4 of 24	5		ENSP00000251041.5

Frequencies

GnomAD3 genomes AF: 0.0805 AC: 12223 AN: 151858 Hom.: 632 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0225

Gnomad FIN AF: 0.0638

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0830

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

GnomAD4 genome AF: 0.0804 AC: 12223 AN: 151976 Hom.: 632 Cov.: 32 AF XY: 0.0763 AC XY: 5673 AN XY: 74306

African (AFR) AF: 0.0360 AC: 1494 AN: 41454

American (AMR) AF: 0.0902 AC: 1378 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 336 AN: 3462

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5138

South Asian (SAS) AF: 0.0221 AC: 106 AN: 4802

European-Finnish (FIN) AF: 0.0638 AC: 675 AN: 10580

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 7991 AN: 67948

Other (OTH) AF: 0.0821 AC: 173 AN: 2106

Alfa AF: 0.0850 Hom.: 100

Bravo AF: 0.0802

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.22
PhyloP100		-1.7
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: rs878536; hg19: chr13-109431493;