rs7997013

Variant names:

• chr13-109051154-T-A
• rs7997013
• NM_001198950.3:c.2873-1146T>A

Your query was ambiguous. Multiple possible variants found:

• chr13-109051154-T-A
• chr13-109051154-T-C
• chr13-109051154-T-G

Variant summary

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

The NM_001198950.3(MYO16):​c.2873-1146T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,960 control chromosomes in the GnomAD database, including 10,724 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 (10724 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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.2873-1146T>A		intron	N/A	NP_001185879.1	F8W883
	MYO16	NM_015011.3		c.2807-1146T>A		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.2873-1146T>A		intron	N/A	ENSP00000401633.3	F8W883
	MYO16	ENST00000356711.7	TSL:1	c.2807-1146T>A		intron	N/A	ENSP00000349145.2	Q9Y6X6-1
	MYO16	ENST00000375857.6	TSL:2	n.2193-1146T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54623 AN: 151842 Hom.: 10717 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.360 AC: 54644 AN: 151960 Hom.: 10724 Cov.: 32 AF XY: 0.370 AC XY: 27491 AN XY: 74268

African (AFR) AF: 0.278 AC: 11528 AN: 41446

American (AMR) AF: 0.465 AC: 7107 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3468

East Asian (EAS) AF: 0.825 AC: 4261 AN: 5162

South Asian (SAS) AF: 0.446 AC: 2145 AN: 4810

European-Finnish (FIN) AF: 0.420 AC: 4427 AN: 10548

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22695 AN: 67948

Other (OTH) AF: 0.357 AC: 753 AN: 2108

Alfa AF: 0.203 Hom.: 405

Bravo AF: 0.364

Asia WGS AF: 0.608 AC: 2114 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	0.33
DANN	Benign	0.38
PhyloP100		-0.60
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: rs7997013; hg19: chr13-109703502;