rs984300

Variant names:

• chr13-108803487-G-A
• rs984300
• NM_001198950.3:c.742-3192G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-108803487-G-A
• chr13-108803487-G-C
• chr13-108803487-G-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.742-3192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,966 control chromosomes in the GnomAD database, including 15,670 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 0.43 (15670 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.742-3192G>A		intron_variant	Intron 6 of 34	ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.742-3192G>A		intron_variant	Intron 6 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.676-3192G>A		intron_variant	Intron 6 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.676-3192G>A		intron_variant	Intron 6 of 24	5		ENSP00000251041.5
MYO16	ENST00000375857.6	n.62-3192G>A		intron_variant	Intron 1 of 21	2

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65573 AN: 151846 Hom.: 15651 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.432 AC: 65603 AN: 151966 Hom.: 15670 Cov.: 32 AF XY: 0.436 AC XY: 32429 AN XY: 74300

African (AFR) AF: 0.227 AC: 9397 AN: 41452

American (AMR) AF: 0.505 AC: 7697 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3468

East Asian (EAS) AF: 0.630 AC: 3255 AN: 5168

South Asian (SAS) AF: 0.502 AC: 2420 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5458 AN: 10546

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34110 AN: 67956

Other (OTH) AF: 0.454 AC: 956 AN: 2108

Alfa AF: 0.468 Hom.: 36404

Bravo AF: 0.427

Asia WGS AF: 0.531 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.52
PhyloP100		-0.93
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: rs984300; hg19: chr13-109455835;