rs40979

Variant names:

• chr5-16721197-A-C
• rs40979
• NM_012334.3:c.1930-9952T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-16721197-A-C
• chr5-16721197-A-G
• chr5-16721197-A-T

Variant summary

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

The NM_012334.3(MYO10):​c.1930-9952T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,130 control chromosomes in the GnomAD database, including 53,384 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 0.84 (53384 hom., cov: 32)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 4 publications found

Genes affected

MYO10 (HGNC:7593): (myosin X) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-10 (MYH10). Unconventional myosins contain the basic domains of conventional myosins and are further distinguished from class members by their tail domains. This gene functions as an actin-based molecular motor and plays a role in integration of F-actin and microtubule cytoskeletons during meiosis. [provided by RefSeq, Dec 2011]

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 = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3	c.1930-9952T>G		intron_variant	Intron 19 of 40	ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.1861-9952T>G		intron_variant	Intron 18 of 39		XP_006714538.1
MYO10	XM_005248307.3	c.1-9952T>G		intron_variant	Intron 1 of 22		XP_005248364.1
MYO10	XM_011514046.3	c.1-9952T>G		intron_variant	Intron 1 of 22		XP_011512348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.1930-9952T>G		intron_variant	Intron 19 of 40	1	NM_012334.3	ENSP00000421280.1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127059 AN: 152012 Hom.: 53351 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.836 AC: 127144 AN: 152130 Hom.: 53384 Cov.: 32 AF XY: 0.836 AC XY: 62188 AN XY: 74354

African (AFR) AF: 0.804 AC: 33378 AN: 41502

American (AMR) AF: 0.826 AC: 12624 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3129 AN: 3468

East Asian (EAS) AF: 0.860 AC: 4449 AN: 5172

South Asian (SAS) AF: 0.678 AC: 3251 AN: 4798

European-Finnish (FIN) AF: 0.884 AC: 9365 AN: 10596

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58259 AN: 67998

Other (OTH) AF: 0.838 AC: 1770 AN: 2112

Alfa AF: 0.847 Hom.: 174162

Bravo AF: 0.831

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.44
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: rs40979; hg19: chr5-16721306;